PCMODEL V 9.0

Transcription

PCMODEL V 9.0

PCMODEL V 9.0
Molecular Modeling Software
for
Windows Operating System
Apple Macintosh OS
Linux and Unix
Serena Software
Box 3076
Bloomington, IN 47402-3076
(812)-333-0823
© 1993-2004 Serena Software. All rights reserved.
First Edition June 1998
Second Edition June 1999
Third Edition January 2001
Fourth Edition April 2002
Fifth Edition August 2003
Sixth Edition August 2004
Trademarks
IBM and IBM PC are registered trademarks of International Business Machines Inc.
Windows is a registered trademark of the Microsoft Corporation.
Alchemy and Sybyl are registered trademarks of Tripos Associates, Inc.
Chem-3D is a registered trademark of Cambridge Scientific Computing, Inc.
ISIS is a trademark of MDL Information Systems, Inc.
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License Agreement
Serena Software provides these programs and licenses their use in your teaching
and research. You assume responsibility for the use of the program to achieve your
intended results.
You may:
1.
Use the programs on any machine or machines in your possession.
2.
Copy the programs and source code into any machine readable form for
backup or modification purposes in support of your use of the programs.
3.
Modify the programs and source code or merge them into another program
for your use. (Any portion of these programs or source code or merged programs
resulting will continue to be subject to the terms and conditions of this
agreement.)
You may not:
1.
Give copies of these programs to anyone else, unless you destroy all
copies you have in any form.
2.
Sell copies of these programs.
3.
Use the programs on a network, unless others are prevented from
accessing the programs.
This license is effective until terminated. You may terminate it at any time by
destroying the programs and source code together with all copies, modifications and
merged portions in any form.
These programs are provided "AS IS" and without warranty of any kind, either
expressed or implied. The entire risk as to the quality and performance of the programs
is with the user.
Serena Software does not warrant the operation of the programs will be
uninterrupted or error free. If Serena Software is unable to deliver a copy of the
programs that is satisfactory, you may obtain a full refund by returning all the program
materials and documentation within 30 days of date of delivery.
These programs are intended for use in chemical research and teaching. Serena
Software will not be liable in any event to you for any damages, including any lost
profits, lost savings or other incidental or consequential damages arising out of the use or
inability to use these programs even if Serena Software has been advised of the
possibility of such damages, or for claim by any other party.
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Table of Contents
Table of Contents ....................................................................................................................................... 4
Chapter 1. Overview.................................................................................................................................. 9
1.1 Introduction ..................................................................................................................................... 9
1.2 Changes in Version 7 ........................................................................................................................ 9
1.3 Changes in Version 7.5 ..................................................................................................................... 9
1.40 Changes in Version 8.0 ................................................................................................................. 10
1.5 History............................................................................................................................................ 10
1.6 The PCMODEL Window............................................................................................................... 12
1.7 Definitions ..................................................................................................................................... 13
1.8 Closing Notes ................................................................................................................................. 13
Chapter 2. Installation.............................................................................................................................. 15
2.1 Windows Installation ...................................................................................................................... 15
2.2 Macintosh Installation..................................................................................................................... 15
2.3 Linux Installation............................................................................................................................ 16
2.4 General Comments ......................................................................................................................... 17
Chapter 3. Quick Summary of PCMODEL Menu Bar Functions .............................................................. 19
Chapter 4. Tutorials ................................................................................................................................. 25
4.1 Methylcyclohexane......................................................................................................................... 25
4.1.1 Drawing the Structure .............................................................................................................. 25
4.1.2 Building the Structure .............................................................................................................. 28
4.1.3 Minimizing and Adjusting the Structure ................................................................................... 29
4.2 Trans-Decalin ................................................................................................................................ 30
4.3 Special Options............................................................................................................................... 31
4.3.1 Compare .................................................................................................................................. 31
4.3.2 Rotational Energy Barriers ....................................................................................................... 32
4.4 Benzene and a Pi Calculation .......................................................................................................... 32
4.5 Biphenyl and a Pi Calculation ......................................................................................................... 32
4.6 Ferrocene - Using Metals and Coordination .................................................................................... 33
4.7 The Methanol dimer - Hydrogen Bonding and Docking .................................................................. 33
4.8 Substructures - Creation and Manipulation...................................................................................... 34
4.8.1 Building Polystryene using Dummy Atoms.............................................................................. 35
4.9 Diels-Alder Transition State............................................................................................................ 35
Chapter 5. Drawing Tools........................................................................................................................ 38
5.1.1 Select Atom ................................................................................................................................. 38
5.1.2 Select Bond.................................................................................................................................. 38
5.2 Draw............................................................................................................................................... 38
5.3 Build............................................................................................................................................... 39
5.4 Update ............................................................................................................................................ 39
5.5 H/AD.............................................................................................................................................. 39
5.6 Add_B ............................................................................................................................................ 39
5.7 In .................................................................................................................................................... 39
5.8 Out ................................................................................................................................................. 39
5.9 Del.................................................................................................................................................. 40
5.10 Move ............................................................................................................................................ 40
5.11 Rotate Bond .................................................................................................................................. 40
5.12 Query............................................................................................................................................ 40
5.13 PT................................................................................................................................................. 41
5.14 Metals........................................................................................................................................... 41
5.15 Rings ............................................................................................................................................ 42
5.16 AA................................................................................................................................................ 42
5.17 Su ................................................................................................................................................. 42
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5.18 Nu................................................................................................................................................. 43
5.18 Organo Metallics Templates.......................................................................................................... 43
5.20 Transition State Templates............................................................................................................ 44
Chapter 6. Conformational Searching ....................................................................................................... 46
6.1 Setup Rings..................................................................................................................................... 47
6.2 Setup Bonds.................................................................................................................................... 48
6.3 Setup Query.................................................................................................................................... 48
6.4 Comparison Method........................................................................................................................ 49
6.5 Options ........................................................................................................................................... 50
6.6 Run GMMX ................................................................................................................................... 50
6.7 Run 2nd Cycle.................................................................................................................................. 51
6.8 Save Job ......................................................................................................................................... 51
6.9 Read Job ......................................................................................................................................... 51
Chapter 7. File Menu ................................................................................................................................ 53
7.1 Open............................................................................................................................................... 53
7.2 Save................................................................................................................................................ 56
7.3 Save Graphic .................................................................................................................................. 60
7.4 Save Movie..................................................................................................................................... 60
7.5 Print................................................................................................................................................ 60
7.6 Read pcmod.bak ............................................................................................................................. 61
7.7 Exit................................................................................................................................................. 61
Chapter 8 Edit Menu ................................................................................................................................ 63
8.1 Draw............................................................................................................................................... 63
8.2 Erase............................................................................................................................................... 64
8.3 Structure name................................................................................................................................ 64
8.4 Hide Hydrogens .............................................................................................................................. 64
8.5 Epimer ............................................................................................................................................ 64
8.6 Enatiomer ....................................................................................................................................... 64
8.7 Remove LP ..................................................................................................................................... 64
8.8 Retype ............................................................................................................................................ 64
8.9 Set Atom Type................................................................................................................................ 65
8.10 List Atom Types ........................................................................................................................... 65
8.11 Read Pcmod.out............................................................................................................................ 65
8.12 Read Pcmod.err............................................................................................................................. 65
8.13 Copy_To_Clipboard ..................................................................................................................... 65
8.14 Orient_XY Plane .......................................................................................................................... 65
8.15 Build Solvent Box/Solvate ............................................................................................................ 65
8.16 Build Periodic Box........................................................................................................................ 66
Chapter 9 View Menu............................................................................................................................... 69
9.1 Control Panel .................................................................................................................................. 69
9.2 Labels ............................................................................................................................................. 70
9.3 Mono/Stereo ................................................................................................................................... 71
9.4 Stick Figure .................................................................................................................................... 71
9.5 Ball and Stick ................................................................................................................................. 71
9.6 Pluto ............................................................................................................................................... 71
9.7 Tubes.............................................................................................................................................. 71
9.8 CPK_Surface .................................................................................................................................. 71
9.9 Dot_Surface.................................................................................................................................... 72
9.10 Ribbon .......................................................................................................................................... 72
9.11 Red/Green Stereo.......................................................................................................................... 72
9.12 Top View...................................................................................................................................... 72
9.13 Dipole Vector ............................................................................................................................... 72
Chapter 10 Compute and Force Field Menus ........................................................................................... 74
10.1 Minimize ...................................................................................................................................... 75
10.2 Single Point .................................................................................................................................. 76
10.3 Use External Charges.................................................................................................................... 76
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10.4 Use Gasteiger Charges .................................................................................................................. 76
10.5 Normal Vibrational Modes............................................................................................................ 76
10.6 Mopac........................................................................................................................................... 76
10.7 Ampac .......................................................................................................................................... 77
10.8 Gaussian ....................................................................................................................................... 77
10.9 Gamess ......................................................................................................................................... 77
10.10 Orbitals ....................................................................................................................................... 78
10.11 Vibrations ................................................................................................................................... 78
10.12 GMMX ....................................................................................................................................... 78
10.13 Metropolis-MC ........................................................................................................................... 78
10.14 Vibrational Mode Search............................................................................................................. 78
10.15 Dynam ........................................................................................................................................ 79
10.16 Auto Dock .................................................................................................................................. 79
10.17 Manual Dock .............................................................................................................................. 80
10.18 Batch .......................................................................................................................................... 81
10.19 Rot_E.......................................................................................................................................... 81
10.20 Dihedral Driver ........................................................................................................................... 82
10.21 Relaxed Grid Search ................................................................................................................... 83
Chapter 11 Analyze Menu ........................................................................................................................ 85
11.1 Surface Area ................................................................................................................................. 85
11.2 Volume ......................................................................................................................................... 85
11.3 Connolly Surface .......................................................................................................................... 85
11.4 Compare ....................................................................................................................................... 85
11.5 Dihedral Map................................................................................................................................ 87
11.6 Movie ........................................................................................................................................... 87
11.7 Dot Map........................................................................................................................................ 87
11.8 MultiStructure............................................................................................................................... 88
11.9 Assign Symmetry.......................................................................................................................... 89
Chapter 12 Substr Menu ........................................................................................................................... 91
12.1 Read ............................................................................................................................................. 91
12.2 Create ........................................................................................................................................... 91
12.3 Move ............................................................................................................................................ 91
12.4 Connect ........................................................................................................................................ 92
12.5 Fuse .............................................................................................................................................. 92
12.6 Erase............................................................................................................................................. 92
12.7 Show Dummy ............................................................................................................................... 92
12.8 Don't Minimize ............................................................................................................................. 93
Chapter 13 Mark Menu............................................................................................................................. 95
13.1 H_Bonds....................................................................................................................................... 95
13.2 Pi Atoms....................................................................................................................................... 95
13.3 Metal Coordination ....................................................................................................................... 96
13.4 TS_Bond Orders ........................................................................................................................... 96
13.5 Fix_Distances ............................................................................................................................... 96
13.6 Fix Angle...................................................................................................................................... 97
13.7 Fix_Torsions................................................................................................................................. 97
13.8 Reset............................................................................................................................................. 97
Chapter 14 Options Menu......................................................................................................................... 99
14.1 Printout ......................................................................................................................................... 99
14.2 Dielc ............................................................................................................................................. 99
14.3 DPDP ........................................................................................................................................... 99
14.4 Minimizer ................................................................................................................................... 100
14.5 MMX_PI Calculation Options..................................................................................................... 100
14.6 Added Constants ......................................................................................................................... 101
14.7 Standard Constants...................................................................................................................... 101
14.8 Stereo ......................................................................................................................................... 101
14.9 Pluto ........................................................................................................................................... 101
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14.10 Vdw Surface ............................................................................................................................. 102
14.11 Dot Surface ............................................................................................................................... 102
15 The MMX Force Field....................................................................................................................... 105
15.1 The MMX Force Field ................................................................................................................ 105
15.2 Minimization with PCMODEL (hints) ........................................................................................ 107
15.3 Transition State Atoms............................................................................................................... 108
15.4 Pi Calculations ............................................................................................................................ 109
15.4.1 Pi Atoms .............................................................................................................................. 109
15.4.2 Heat of Formation of Pi Systems .......................................................................................... 110
15.5 Transition Metals ........................................................................................................................ 111
Chapter 16 File Formats ........................................................................................................................ 114
16.1 PCM File Format ........................................................................................................................ 114
16.2 MMX Input Files ........................................................................................................................ 119
16.3 Mopac and Ampac Files.............................................................................................................. 135
16.4 X-RAY Files............................................................................................................................... 136
16.5 SDF and Mdl Mol Files............................................................................................................... 137
16.6 Chem3D and Tinker Files ........................................................................................................... 137
16.7 Cambridge Structural Database Files........................................................................................... 137
16.8 Alchemy and Sybyl Mol Files ..................................................................................................... 137
16.9 Gaussian Input and Output Files.................................................................................................. 137
16.10 Gamess Input and Output Files.................................................................................................. 137
16.11 ADF, PQS, Hondo and Turbomole Files ................................................................................... 137
16.12 Smiles Files .............................................................................................................................. 137
Chapter 17 Parameter Files..................................................................................................................... 138
17.1 Overview .................................................................................................................................... 138
17.2 Atom Types ................................................................................................................................ 139
17.3 Bonds ......................................................................................................................................... 139
17.4 Angles ........................................................................................................................................ 140
17.5 Stretch-Bend ............................................................................................................................... 141
17.6 Torsions...................................................................................................................................... 141
17.7 Van der Waals ............................................................................................................................ 142
17.8 Charge and Dipole ...................................................................................................................... 142
17.9 MM3 Specific ............................................................................................................................. 142
17.10 Pi Calculations .......................................................................................................................... 143
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Chapter 1. Overview
1.1 Introduction
PCMODEL is an interactive molecular modeling program for the study of organic and
inorganic molecules. PCMODEL is simple to use and has a number of structure creation, display
and energy minimization options. In this manual, we will discuss installation of the program, the
features of the various menus, the different force fields supported by PCMODEL, and the formats
of the various files that can be read and written. A short tutorial on structure building and
manipulation is also included. A complete discussion of the methods of molecular mechanics is
beyond the scope of this manual. General information about molecular mechanics can be found in
the book "Molecular Mechanics", U. Burkert and N. L. Allinger, ACS Monograph Series, Number
175 and in "A Handbook of Computational Chemistry: A Practical Guide to Chemical Structure
and Energy Calculations", by Tim Clark, J. Wiley and Sons, 1985. More current information can
be found in "Journal of Computational Chemistry", edited by N. L. Allinger and the book series
"Reviews in Computational Chemistry", edited by K. Lipkowitz and D. B. Boyd.
1.2 Changes in Version 7
Version 7 of PCMODEL introduces several major changes; the most important of which is
the addition of support for other force fields. The current release supports the MM3 and MMFF94
force fields in addition to the MMX force field that was in earlier versions of PCMODEL. Planned
for future releases is support for the Amber, Charmm and OPLS force fields. In order to support
additional force fields we have rewritten the entire force field section of the code, added new
minimizers and changed the format of the parameter files. Version 7 includes both a first derivative
minimizer and also a full-matrix second-derivative minimizer.
1.3 Changes in Version 7.5
Version 7.5 of PCMODEL introduces several additional changes. The current release now
supports the AMBER force field. Additional items have been added to the Menu Bar. Some items
under the View and Compute options have been moved to a new Analyze menu item. The View
options now include the ability to change the screen background color, to view structures in red and
green stereo, to have a small top view of the structure and to display a dipole vector. The Analyze
menu options have added the ability to display the molecular symmetry, and view/analyze multiple
structure files. With the multiple structure option one may view in sequential or random order a
multiple structure file. One may also do a query on a set of structures, extract structures which
match a query or do a global comparison of all structures in a file. The Compute menu option has
added the ability to do normal vibration mode calculations and the ability to do conformational
searches using low-mode vibrations. The use of solvents has also been improved.
Version 8.0 of PCMODEL includes support for the Oplsaa force field, reading Gaussian
Formatted checkpoint files, reading and writing Hondo files. In the Compute Menu there are
options to use charges read from a structure file or Gasteiger charges rather than the default force
field charges. There is a Manual Docking option, and there are more options for running Batch
calculations. The ability to change the atom colors and the background colors has been added to the
Options Menu
Version 8.5 of PCMODEL adds support for the PQS, ADF and Turbomol quantum
chemistry programs. In the File Menu there is now an option to save Movie files, under the Save
Graphics option there is support for PovRay files. In the Edit Menu there is support for reading the
Pcmod.Err and Pcmod.Out files so that errors due to missing constants can be checked without
exiting PCMODEL. In the View Menu there is an option to show the Backbone of a polypeptide
and in the Compute Menu an option for a Relaxed Grid Search. In the Analyze Menu there is an
option for calculating surface areas and volumes using the Connolly algorithms, and there is further
support for analyzing multiple structure files. The Templates Menu now contains a set of
Heterocycles and the Substr Menu now has a Fuse option for fusing two rings.
Version 9.0 of PCMODEL has a completely rewritten graphics engine based on OpenGL.
This greatly improves rendering of screen images. Highlighting of atoms or bonds is now visible in
Stick Figure, Ball and Stick and CPK views. The format of the ouput window has been changed.
The Movie option now reads Gaussian 03 formatted checkpoint files for IRC calculations. Two
dimensional SDF files, such as those output by Isis Draw, that contain stereochemical information
can now be converted to three dimensional structures. In the Edit Menu there is now an option to
Set the atom type of a specific atom, and also an option to List all the atom types in the current
force field. In the Options menu the user can now reset the paths which point to external programs
such as Gaussian, Gamess or Mopac.
1.5 History
PCMODEL is derived from several sources. The graphical user interface originally came
from MODEL, written by C. Still. It has been extensively modified for PCMODEL for WindowsTM.
MODEL was ported to the IBM-PC and renamed PCMODEL by M. Mark Midland, University of
California, Riverside, J.J. Gajewski of Indiana University, Kosta Steliou of Boston University and
K.E. Gilbert of Serena Software. K. E. Gilbert, J. J. Gajewski and T.W. Kreek of Indiana
University then ported PCMODEL to the Macintosh, Silicon Graphics and Sun workstations. K.E.
Gilbert wrote the current version of PCMODEL for Windows, the Apple Macintosh, Unix and
Linux.
The default force field used in PCMODEL is called MMX and is derived from MM2
(QCPE-395, 1977) force field of N. L. Allinger, with the pi-VESCF routines taken from MMP1
10
(QCPE-318), also by N. L. Allinger. J. McKelvey of Kodak modified the pi-VESCF routines for
open shell species, while J. J. Gajewski did improvements to the heat of formation calculations.
MMX increased the number of atom types for the MM2 force field, added the ability to handle
transition metals and transition states, and increased the number of parameters included in the
database. J. J. Gajewski and K. E. Gilbert made these changes.
Algorithms to compute surface areas and volumes using a Monte Carlo method were
provided by Professor William Herndon of the University of Texas at El Paso.
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1.6 The PCMODEL Window
PCMODEL uses a standard window in all versions of the program. The main window in the
WindowsTM version is shown below.
A menu bar appears at the top of the screen, with 10 options - FILE, EDIT, VIEW,
COMPUTE, ANALYZE SUBSTR, TEMPLATES, MARK, OPTIONS, FORCE FIELD and
HELP. The commands under each of these headings are described in detail in later chapters. A
second bar of drawing tools appears along the right hand edge of the screen (this is referred to as
the TOOLS menu or Drawtools menu) The Drawtools menu may be moved. At the bottom of the
screen is a status bar, which indicates the status of various options.
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1.7 Definitions
Within this manual, the terms window and screen will be used interchangeably to refer to
the main graphics window in which PCMODEL is running.
The term attached atom refers to an atom with only one connection, such as hydrogen
attached to a carbon. A connected atom is one that is connected to the given atom and may include
an attached atom.
Pointing, clicking, hitting or pressing a button all refer to a single click of the left mouse
button over the word, button, atom or bond.
A substructure is a collection of atoms that may or may not be connected, that have a
common value among their substructure numbers and an associated name. Substructures can be
moved, rotated, connected, hidden, minimized independently, and docked to one another or to a
main structure. When written with a PCM file format, substructure information is maintained, so
substructures can be stored. A single atom may belong to more than one substructure. When a
substructure is connected to another structure, a bond is formed but the substructure information is
maintained. Thus, a substructure can be part of a contiguous structure, and when the structure is
moved or rotated the joining bond can be stretched abnormally. Remember that, when connecting
substructures, the substructure that is chosen many not be the entire connected structure, thus
leading to the stretch of one bond in order to form the connected bond.
1.8 Closing Notes
This manual describes only a few of the possible chemical structures that we can study with
PCMODEL. We have tried to do the very best job of representing chemistry with a computer
model. No doubt there are many problems still remaining and many faults with our models. If you
find problems, or think the calculations are incorrect, please let us know. We are always trying to
improve the chemistry of PCMODEL and since we are few and the problems are many, your help
is always appreciated. We can be reached at:
Phone
(812)-333-0823
FAX
(812)-332-0877
Email
[email protected]
WWW
http://www.serenasoft.com/
Mail
Serena Software
Box 3076
Bloomington, IN 47402-3076
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Chapter 2. Installation
2.1 Windows Installation
This manual assumes a basic working knowledge of the operation of your computer system,
and the WindowsTM software. If there are things mentioned which are not clear, consult your
computer's user or system administration help procedures or manuals. PCMODEL for WindowsΤΜ
is shipped as a series of files on a CD.
Installation from a CD
You should first create a directory on your hard disk to contain the PCMODEL program.
Then you will need to copy all the files from the CD into the new folder on the hard disk. The list
of files given below will now be on the hard disk and ready to use. Do not drag the entire CD onto
your hard drive, if you do Windows will mark the resulting folder as a “read only” folder and
Pcmodel will not be able to write backup files and output files into this folder. This will result in
Pcmodel crashing with “write protect”errors.
Pcm9.exe
mmxconst.prm
mm3.prm
mmff94.prm
amber.prm
oplsaa.prm
aa.sst
nu.sst
su.sst
rings.sst
hetero.sst
templt.sst
fg.sst
orgmet.sst
executable copy of PCMODEL
text file containing specific constants used by PCMODEL
file containing MM3 constants used by PCMODEL
file containing MMFF94 parameters
file containing AMBER parameters
file containing Oplsaa parameters
Substructure template files
"
"
"
"
"
"
"
You may now return to WindowsΤΜ and use the TaskbarΤΜ setup from the Setting option in
the Start Menu to install the PCMODEL icon. In the Taskbar properties dialog box choose the
Start Menu Programs and then choose Add to add a new item to the Task Bar. Use the Browse
option to search for pcm9.exe, then select the program group for the icon or create a new program
group.
2.2 Macintosh Installation
PCMODEL for the Macintosh is shipped as the fully expanded program on a CD. Create a
new folder on your hard drive and drag the files from the CD onto the hard drive. The files are
listed above with the only change being the in the program name:
Pcm9.app
OS X version of PCMODEL
If you drag the entire CD onto your hard drive OS X will mark the new folder as write protected
and Pcmodel will crash when you try to minimize anything, so just copy the contents of the CD.
Also, OS X treats the forward slash, ‘/’, as a special character (as does Unix and Linux) and you
can not use it in folder names. If you do Pcmodel will not start. The constants files, *.prm, contain
the parameters used in the calculations. These are text files that can be read and edited with a word
processor to make parameter editing and addition easier. Please be certain to save these files as text
only files when editing them with a word processor like Microsoft Word. If you save them as a
standard Word document they will have formatting information embedded in the file and will not
be read properly by PCMODEL. Using a simple, non-formatting text editor, such as Teach Text, is
recommended. When Pcmodel starts it will locate the folder it resides in and will also get the
current working folder from OSX and it will write the output and backup files into the current
working folder. Thus it is possible to install Pcmodel into a write-protected area and to have
multiple users accessing the program. The output for each user will usually be placed in the users
document folder, ie /Users/usename/documents.
2.3 Linux Installation
PCMODEL for Linux or Unix is shipped in as a compressed tar archive, pcm9_linux.tar.gz.
Copy this file to the hard drive on your computer, unzip it using gunzip and then extract the files
from the tar archive. The standard commands would be (assuming you are logged into your home
directory):
Cp /mnt/cdrom/pcm9_linux.tar.gz .
Gunzip pcm9_linux.tar
Tar xvf pcm9_linux.tar
PCMODEL uses X and OpenMotif on Linux, however, the executables are statically linked and
you will need to have Motif or Lesstif installed only if you will be recompiling the source code.
The latest version of Lesstif can be obtained from www.lesstif.org and OpenMotif from
www.openmotif.org .Pcmodel now uses OpenGL for the graphics engine and uses the current
screen depth automatically. The source code is included along with a Makefile. Please consult your
Linux documentation if you have not installed all the libraries necessary.
Pcmodel can use the environment variable PCM_DIR to locate the parameter and template
files. If the PCM_DIR variable is not defined Pcmodel will look in the current working directory
for these files. The output and backup files will be written to the current working directory.
The Linux version of PCMODEL has been tested with RedHat (up to version 7), SuSE (v 9)
and Mandrake (v9). Other versions of Linux and other flavors of Unix can be supported by
recompiling the source code. We have recompiled the current source code on SGI and HPUX
computers with only one modification of the source. You will also need to edit the Makefile
included with the source code to use these systems as appropriate for your system.
16
2.4 General Comments
You are now ready to run PCMODEL by double clicking on the PCMODEL icon.
PCMODEL normally only uses sixteen colors for drawing structures, however if you want good
CPK surfaces you should set your monitors control to Millions of colors (if possible), otherwise use
256 colors. This will have no effect on normal operation of PCMODEL. There are some
fundamental hardware differences between a PC, a Macintosh and Linux, such as the Macintosh
having only a one button mouse while the PC normally uses a three button mouse. Where this is
important we will make a comment in the documentation, but we have tried to make the three
versions as similar as we can so functions should look and feel the same in the Windows,
Macintosh and Linux versions.
17
18
Chapter 3. Quick Summary of PCMODEL Menu Bar
Functions
File Menu
Open
Save
SaveGraphic
SaveMovie
Print
Read pcmod.bak
Exit
Edit Menu
Draw
Erase
Structure Name
Hide Hydrogens
Epimer
Enantiomer
Remove LP
Retype
Set Atom Type
List Atom Type
Read Pcmod.Out
Read Pcmod.Err
Copy_To_Clipboard
Reads a file from disk.
Saves a file to disk
Saves a graphics image to a disk file
Saves a Movie to a disk file
Prints the current structure and energy windows
Read pcmod.bak file
Exits PCMODEL
Recovers the TOOLS menu
Erases all structures
Edit or enter name of current structure
Make the hydrogens in a structure invisible
but still present
Epimerizes the selected atom by interchanging the
two selected attachments.
Reflects the structure through a specified axis
Remove lone pairs from a structure.
Forces PCMODEL to reassign atom types.
Set the atom type of the selected atom and prevent
retyping this atom.
List the atom types in the current force field.
Read Pcmod.Out file using simple text editor
Read Pcmod.Err file using simple text editor when
missing constants error message is shown.
Copies an image of the structure window to the
clipboard.
Orient_XY
Orient_XZ
Orient_YZ
Orients the selected three atoms in the XY Plane with the
first atom at the origin the second atom along the axis and the
third atom in the plane.
Build Solvent Box/Solvate
Build a box of solvent molecules or solvate the current
structure.
Build Periodic Box
Build a box of the current structure.
View Menu
Control Panel
Labels
Brings up a dialog box to scale, translate and rotate
structures in the structure window.
Dialog box to change the structure labels
19
Mono/Stereo
Stick Figure
Ball and Stick
Pluto
Tubular Bonds
CPK Surface
Dot Surface
Ribbon
BackBone
RedGreen Stereo
Top View
Dipole Vector
Compute Menu
Minimize
Single Point
Use External Charges
Use Gasteiger Charges
Use GB/SA Model
Normal Vibrational Modes
Mopac
Ampac
Gaussian
Gamess
Toggles between mono and stereo display
Display all structures as stick figures.
Display all structures as ball and stick.
Display all structures as Pluto type ball and stick.
Display all structures as Tubes.
Display all or selected structures with CPK surface.
Display all or selected structures with dot surface.
Ribbon diagram of peptide or nucleic acid backbone
Display a Backbone picture of peptide.
Sets view to red/green stereo
Turns on top view of current structure
Draws a dipole moment vector on current structure.
Minimize the current structure(s).
Calculate the energy of the current structure(s).
Use charges read from Mopac or Ampac file
Use charges generated by Gasteiger sigma model
Use generalized Born salvation model
Compute normal vibrational modes
Runs the quantum chemistry program Mopac.
Runs the quantum chemistry program Ampac
Runs the quantum chemistry program Gaussian.
Runs the quantum chemistry program Gamess.
Orbitals
Runs the Orbdraw program to view molecular orbitals and
electron densities
Vibrations
Runs the Vibrate program to view normal
vibrational modes
GMMX
Runs the conformational searching program on the current
structure.
Metropolis MC
Runs conformational search using Monte Carlo
algorithm
Vibrational Mode Search
Runs conformational searching using low frequency
vibrational modes as search directions.
Dynam
Auto Dock
Molecular Dynamics simulation.
Simulated annealing search of lowest energy
interaction between two structures.
Manually move two structures to dock them
Read a multiple structure file and minimize all
structures.
Rigid rotor evaluation of rotational energy barrier.
Grid search with minimization evaluation of
rotational energy barrier.
Use Grid Search as starting point for Minimization
but no fixed dihedrals
Manual Dock
Batch
Rot_E
Dihedral Driver
Relaxed Grid Search
Analyze Menu
20
Surface Area
Volume
Connolly Surface
Compare
Dihedral Map
Calculate Surface area of molecule.
Calculate Volume of molecule.
Use Connolly algorithms for surface area and
volume
Compare different structures.
Display the results of dihedral driver calculations.
Movie
Replay the structures contained in a multiple structure file.
Currently supports PCM, MMX, Gaussian and Cambridge
Structural Database file formats.
Dot Map
Multi Structure File
Assign Sym
Generate a dot map from a multi conformation file.
Analyze a file containing multiple structures.
Assign point group symmetry to current structure.
Substr Menu
Read
Create
Move
Connect
Fuse
Erase
Show Dummy
Don't Minimize
Templates Menu
Rings
Amino Acids
Sugar
Nucleosides
Heterocycles
OrganoMetallics
Transition State
Functional Groups
Mark Menu
H Bonds
Pi Atoms
Metal Coord
TS_BondOrders
Fix Distance
Fix Angle
Fix Torsions
Equivalent Pi Atoms
Read a structure file and label the structure as a
substructure.
Label the selected structure as a substructure
Move the selected substructure.
Connect two structures.
Fuse two rings.
Erase the selected substructure
Displays dummy atoms in current structure.
Mark the selected substructure so that it will not be
minimized in a molecular mechanics calculation.
Dialog box to read in selected ring systems.
Dialog box to read in and connect Amino Acids.
Dialog box to read in and connect Sugars.
Dialog box to read in Nucleosides.
Scrolling list of Heterocyclic Rings
Dialog box to read in selected organometallic
structures.
Dialog box to read in selected transition state
models.
Dialog box to read in selected functional groups for
connection to larger structure.
Hydrogen Bonds
Pi atoms.
Set electron count, charge and coordination of metal
atoms.
Set the bond orders for transition state bonds.
Fix a distance between any two atoms
Fix an angle.
Fix a dihedral angle
Mark pi atoms to be made equivalent
21
Create Centroid
Reset
Options Menu
Printout
Dielc
Input/Output Atom Types
DPDP
Minimizer
MMX_Pi Calc
Added Constants
Standard Constants
Stereo
Pluto
CPK Surface
DOT Surface
Change Background Color
Change Atom Colors
Reset Default Paths
Edit PBC
Create a centroid for five and six membered rings.
Reset any of the above and also substructure
membership.
Sets the amount of output in PCMOD.OUT.
Resets the dielectric constant.
Define the atom types to be used in reading/writing
structure file that uses atom types.
Change between dipole-dipole and electrostatic
calculations.
Set options for the minimizers.
Set options for Pi calculation
Allows user defined constants
Rereads the default MMX datafile
Changes the direction of rotation of stereo display.
Sets options for the Pluto Display.
Sets the options for the VDW display.
Sets the options for the DOT surface display.
Change the default color of the Background
Change the default colors of the Atoms.
Reset the paths to external programs.
Edit periodic boundary conditions
Force Field
MMX
MM3*
MMFF94
Amber
Oplsaa
Use the MMX force field.
Use the MM3 force field
Uses the MMFF94 force field.
Uses the Amber 95 force field.
Uses the Oplsaa force field.
Help Menu
About
Help
Current version of PCMODEL
Start a browser to read the Pcmodel documentation.
22
Quick Summary of TOOLS Menu:
Sel-Atm
Sel-Bnd
Draw
Build
Update
H/AD
Add_B
In
Out
Del
Move
Rot-B
Query
PT
Metals
Rings
AA
Su
Nu
OrgMet
TransSt
Select atoms.
Select bonds.
Draw a carbon skeleton in either the plane of the screen or
the plane of the first selected atom.
Generate 3-D structure by replacing selected hydrogen with
methyl group. Starting from ethane, any hydrogen selected
will be replaced by methyl.
Update the structure and redraw the screen.
Add and delete hydrogens and lone pairs.
Increment the bond order of the selected bond.
Push an atom into plane of screen.
Pull atom out of plane of the screen.
Delete an atom or bond.
Move an atom. Select Move, then atom, then new position.
Rotate about the bond selected by four connect atoms.
Query selected position, charge, POAV, distance, angle or
dihedral. Works by first selecting Query, then selecting
one, two, three or four atoms followed by blank space in
drawing window. Queries removed by selecting Update
button twice.
Dialog box to choose atom type.
Dialog box to choose metal atom type.
Dialog box to read in selected ring systems.
Dialog box to read in (and connect) Amino Acids.
Dialog box to read in (and connect) Sugars.
Dialog box to read in Nucleosides.
Dialog box to read in OrganoMetallic structures
Dialog box to read in transition state models.
23
24
Chapter 4. Tutorials
PCMODEL is designed to be easy to use. In this chapter the basics of using the program,
along with many of its options, will be covered through example. Before beginning the specific
examples, there are some general points about structure entry to be considered.
The screen is two dimensional. Initial input occurs at 0 on the z-axis. The screen itself is
the xy-plane. Thus, a hexagon drawn to represent cyclohexane using the DRAW Command is
initially flat. To obtain three-dimensional structures you need to move atoms behind or in front of
the z plane with the IN and OUT commands on the TOOLS menu. Once some three-dimensional
information is available, further structural input can be done by rotating the structure. If you pick
an atom and draw a bond to a new atom, the new atom will lie parallel to the picked atom along the
coordinate that is perpendicular to the screen.
Complex structures are easier to build using the substructure ADD, ROTATE and MOVE
commands. You can use the built-in substructure templates, or build a library of your own by
creating structures and saving the minimized coordinates in an MMX or PCM file.
Options are selected by pointing to the desired option and clicking (move the cursor until it
is over the desired option and click the left mouse button). If the wrong option is chosen, simply
choose the correct one and continue. Likewise, atoms are input or selected by pointing to the
appropriate spot in the drawing box. When the cursor is over an atom the atom will be highlighted
(a box will be drawn around the atom) so you may tell which atom is closest to the cursor.
On the PC the right mouse button may always be used to rotate the current structure.
Holding the right mouse button down and dragging the mouse will cause the structure to rotate.
Moving the mouse to the left or right will rotate about the y-axis, while up and down movement
rotates about the x-axis. Holding down the shift key while dragging the mouse will rotate the
structure about the Z-axis. On the Macintosh simply hold down the mouse button and drag. More
complete control of rotation, translation and scaling is had using the Control panel in the View
Menu.
The following examples will illustrate a few of the options available for structural input,
minimization and display using PCMODEL. A few mistakes will be purposely made along the
way to illustrate how they may be corrected.
4.1 Methylcyclohexane
Structures are drawn on the screen in essentially the same way as they would be represented
as 3-D structures on paper. For example, a hexagon could be drawn. Initially this would be in the
XY plane with all Z coordinates equal to zero. Three-dimensional information could be entered by
using IN to push one atom in to the screen and OUT to place the opposite atom in front of the
screen. Alternatively, OUT could be used to place 3 alternating carbons in front of the screen to
provide a chair shape. In this tutorial, however, we will begin by drawing a side-on view of the
chair form.
4.1.1 Drawing the Structure
25
Begin by selecting the DRAW button on the TOOLS menu with the mouse. A dotted
outline will indicate that you are in Draw mode. Move the cursor off the TOOLS menu and into
the drawing box, somewhere in the upper right hand corner. (We will be drawing cyclohexane as
in Figure 4.1.) Click the mouse button once then move the cursor down ~ 3 cm and left another 3
cm, and click again. A line indicating a bond between the first atom and the one just placed will be
drawn. Continue drawing in this manner, placing atoms 3, 4 and 5.
1
2
3
5
6
4
Figure 4.1 Completed cyclohexane structure with atom numbers displayed.
The atom numbers can be displayed on the screen by choosing LABELS from the VIEW
menu, then clicking in the circle next to "atom numbers" and clicking on "okay". They can be
removed by again choosing LABELS from the VIEW menu, then clicking in the circle next to
"Hydrogens and Lone Pairs"
At this point, we will purposely make a mistake, by connecting atom 2 to atom 5. To get
back into the drawing mode, select DRAW from the TOOLS menu. Then, click on atom 5, then on
atom 2. This will create a bond between atoms 2 and 5. (If the cursor is within about 1/4 inch or
0.5 cm or an atom, then that atom will be picked by the program instead of creating a new one.) To
correct the mistake, move the cursor to the DEL button on the TOOLS menu and click on it. Now
click on the middle of the bond between atoms 2 and 5 (the incorrect bond). The structure will be
redrawn with the deleted bond removed.
To continue drawing, again click on the DRAW button on the TOOLS menu, then click on
atom 5 and continue to draw atom 6 and the bond back to atom 1. At this point the structure should
resemble a chair cyclohexane as in Figure 4.1. However, remember that all the atoms are still in
the plane of the screen, that is, no 3-D information has been included. To fix the structure, choose
OUT from the TOOLS menu, and then click on atom 2 twice. Each click moves the atom 0.33 Å
out of the plane of the screen. Next, point to atom 3 and click 2 times. Now select IN from the
TOOLS menu and click on atom 5 twice and atom 6 once (another mistake which we will shortly
correct). Rotation of the structure by dragging the mouse will reveal the changes in the structure.
The initial view of the molecule is in the XY plane. The Z+ axis comes out towards the
user. To view the structure from a different orientation, select CONTROL_PANEL from the
VIEW menu. A new window entitled "Dials" will appear. Within this window will be continuous
sliders that allow you to change the orientation of the structure. By clicking on the arrow at either
end of a slider once, the view will move slightly. Holding down on one of the arrows will provide
26
continuous movement in that direction. Alternatively, you may click on the box in the middle of
the slider bar, and drag it while holding down with the mouse button. This will also provide
continuous movement of the view until the mouse button is released. The RESET_VIEW button
will return the structure to its original orientation. If you rotate the structure in the Y direction, you
can see how atoms 2 and 3 line up, but atoms 5 and 6 do not (because atom 6 was purposely moved
only once). This could be corrected by returning to the original view, then using IN on atom 6 one
more time. However, we will correct this using the MOVE command from the TOOLS menu.
After selecting MOVE from the TOOLS menu, click on atom 6, then near atom 5 (the position to
which atom 6 should be moved). The structure will be redrawn with the correction.
Hydrogens may be automatically added by selecting the H/AD command from the TOOLS
menu. However, once you have done this, there is no free valence at which to add the methyl
group. This can be corrected in one of two ways. The first alternative is to delete the hydrogens by
clicking on H/AD again, then select DRAW and click on atom 1 then on a blank space to the right
of atom 1 to add the extra methyl group. (If the structure is too large, there will not be room on the
screen to add the methyl group. If this is the case, use the SCALE option, accessed through the
CONTROL_PANEL option of the VIEW menu, to shrink the structure to a more manageable size.)
The structure would them be completed by re-selecting H/AD to add the hydrogens. A second
alternative is to change the equatorial hydrogen into a carbon. Select PT (Periodic Table) from the
Tools menu. Select C from the list of available atom types, and click on the equatorial hydrogen.
Select H/AD to delete hydrogens (but the equatorial carbon will stay), then H/AD again to add
hydrogens. The PERIODIC_TABLE window may be removed be selecting CANCEL (the last
option in this window). This method of replacing specific hydrogens is very useful for controlling
the stereochemistry when building large and complicated structures. A third alternative is to use
the Build command from the Tools. In Build mode clicking on a hydrogen replaces that hydrogen
with a carbon and then does a hydrogen delete/add sequence so the methyl group is added with
only one click of the mouse.
It is not important if the structure does not look perfect at this point. Only a crude
approximation of the structure is needed for minimization. However, the closer to correct the
structure is, the faster the minimization will proceed. Methyl groups pointing in to the middle of a
cyclohexane ring will obviously cause problems. Also, if three carbons are attached to a central
carbon such that all 4 are in a plane, the program will have difficulty in adding a hydrogen in the
correct position. You can check for such errors by using the rotation and translation sliders in the
DIALS box to get different views of the molecule. Use IN, OUT and MOVE from the TOOLS
menu to correct these problems.
Before starting a minimization, it is a good idea to store the structure with a descriptive
filename. Select SAVE from the FILE menu. Select the appropriate file type from the list
provided by clicking on it with the left mouse button. (The default file type of PCM is preferable.)
The "File Name:" box will change to indicate the default extension for that type of file. The "*" in
the file name should be changed to a descriptive name for this structure, for example, etcyclo. The
path indicating where the file is to be saved may also be changed at this time. When the correct
path and filename have been entered, click on "OK" or press return on the keyboard to save the
structure in the indicated location.
At the beginning, every five iterations during, and at the end of the minimization process a
backup file of the structure, called PCMOD.BAK will be written (the format is PCM). If anything
should go wrong or should you need to stop the program, you may restart the minimization by
reading in this file and continuing from the last saved point.
27
4.1.2 Building the Structure
A structure may also be constructed by using the BUILD command of the DRAW TOOLS.
Begin by selecting BUILD. An ethane will appear (Figure 4.2). Click on the upper right hydrogen
to produce propane as shown in Figure 4.3. Next click on hydrogen 10 to provide butane as shown
in Figure 4.4. It may be easier to see the 3-dimensional nature of the structure if you turn on
Tubular Bonds from the View Menu as in Figure 4.5. However it is usually easier to click on
atoms using the stick figure. You can rotate the structure at any time by holding down the mouse
button (right button on the PC) and dragging.
Figure 4.2.
Figure 4.3
Figure 4.4
Continue the build by clicking on the next hydrogen in the sequence to obtain Figure 4.6 and then
to obtain Figure 4.7. Again it may be helpful to turn on Tubular Bonds to see the 3-d structure.
28
Figure 4.5
Figure 4.6
Figure 4.7
Complete the ring by removing the hydrogens (H/AD) and then use Draw to create a bond between
carbon 1 and 6. It does not matter if you draw the bond first or remove hydrogens first. You will
arrive at Figure 8 either way.
Figure 4.8
Figure 4.9.
Figure 4.10
Complete the structure by adding the hydrogens (H/AD) to give Figure 4.9 and then using Build to
add the methyl group (Figure 4.10).
The easiest method for constructing methylcyclohexane is to read C6 from the RINGS
template of the Draw Tools or under Template on the Menu Bar then add the methyl group using
BUILD.
4.1.3 Minimizing and Adjusting the Structure
The structure may now be minimized. Select MINIMIZE from the ANALYZE menu, and
the calculation will automatically start. Once the minimization process has started, pointing to the
Stop Job button may stop it. The cursor will change into an hourglass shape while the
minimization is in progress, and will return to the arrow shape when it is completed. The final
energy should be around 6.89 kcal. Save this structure, as it will be used later.
We now want to compare the energy of the equatorial isomer to that of the axial isomer.
We could start from scratch by clearing the current structure by selecting ERASE from the DRAW
menu, and drawing in a new chair cyclohexane with an axial methyl group. However, it is usually
simpler to modify the present structure. This can be done in several ways. Some choices are:
29
Use MOVE: Select H/AD to remove the hydrogens. Then select MOVE from the TOOLS
menu, and click on the equatorial carbon. Next point to a new position above atom 1 where
the axial group is to be located. Use H/AD again to add the hydrogens back on to the
structure. Check that you have in fact obtained the axial isomer. If not, remove the
hydrogens again and move the carbon atom further.
Use DEL and the Periodic Table: Bring up the Periodic Table by selecting PT from the
TOOLS menu. Choose the C atom, and click on the axial hydrogen to change it into a
carbon. Then select DEL from the TOOLS menu and click on the carbon of the equatorial
methyl group. It, along with the attached hydrogens, will be automatically deleted. Then
click on H/AD twice to remove then replace the hydrogen atoms.
Use DEL and BUILD: Select DEL from the TOOLS menu and click on the carbon of the
equatorial methyl group. It, along with the attached hydrogens, will be automatically
deleted. Then select BUILD and click on the axial hydrogen.
Use EPIMER: Click on Sel-Atm on the TOOLS menu. Then click on carbon 1, then to the
axial hydrogen and equatorial carbon. Small filled circles will indicate that the atoms have
indeed been selected. If hydrogens obscure any of the atoms, use the DIALS box to rotate
the structure to a better orientation, or SCALE it up to zoom in on the area of interest. Then
select EPIMER from the EDIT menu, and the two attached groups will be switched.
Now select MINIMIZE from the ANALYZE menu to find the energy of this structure. It
should be about 8.67 kcal or 1.78 kcal higher than the equatorial isomer. Save this file with a
different filename from that used for the equatorial isomer.
4.2 Trans-Decalin
We will next illustrate how to build up a simple structure by converting axial methyl
cyclohexane into 1-methyl- trans-decalin. Begin by reading in the minimized axial methyl
cyclohexane structure previously saved by choosing OPEN from the FILE menu. Use H/AD to
remove the hydrogens. Turn on atom numbering (LABELS under VIEW menu), bring up the
DIALS box by choosing CONTROL_PANEL from the VIEW menu, and rotate the structure along
the X-axis until it has an orientation similar to that in Figure 4.11. Using DRAW from the TOOLS
menu, click on atom 1, then continue to place atoms 8, 9, 10 and 11, and the final bond back to
atom 2.
30
10
9
11
8
7
2
3
1
6
4
5
Figure 4.11 Completed 1-methyl-trans-decalin structure with atom numbers displayed.
Carbons 8 through 11 will have the same Z coordinate as atom 1, the last atom selected
prior to drawing them. If we had chosen atom 2 as the starting point, then carbons 8 through 11
would have the same Z coordinate as atom 2. Use OUT to push atom 9 out 2 clicks, and IN to
move atoms 10 and 11 each in 4 clicks. Use the rotation and translation sliders to check placement
of the atoms and MOVE to correct any mistakes. Add the hydrogens back with H/AD and proceed
with the minimization.
4.3 Special Options
4.3.1 Compare
The COMPARE option is used to calculate the differences in two structures and to produce
an overlaid view of two structures. Begin with axial methyl cyclohexane as the active structure.
Select COMPARE from the VIEW menu. Select NEXT_STRUCTURE from the COMPARE
menu, and enter the name of the equatorial cyclohexane structure. We will want to see how the
axial and equatorial atoms change positions if the remainder of the ring is held constant. Use the
Sel-Atm button from the TOOLS menu to mark carbons 3,4 and 5 on the left (axial) isomer, then
carbons 3,4 and 5 on the right (equatorial) isomer. The comparison will pair the first atom selected
on the first structure with the first atom selected in the second structure, etcetera, so it is important
to select the atoms in the same order on the two structures. Once the atoms have been selected,
choose CALCULATE from the COMPARE window. PCMODEL will now find the best least
squares fit for these three atoms, and will give the rms differences between all corresponding atoms
in the Compare Output window, and the structures will be redrawn overlapped, with red lines
connecting the atoms that are being compared. If the structures overlap well, the red lines may not
be visible. The structures may be rotated in mono or stereo to get a better view of the comparison.
Select MOVE from the SUBSTR menu, and choose the substructure "untitled". Use the
DIALS box to translate this substructure away from the other one. A new set of atoms for
comparison can now be marked on each substructure (using the Sel-Atm option), and the
calculation re-done. Click on CANCEL to dismiss the COMPARE window.
31
4.3.2 Rotational Energy Barriers
PCMODEL can calculate rotational barriers using the DIHEDRAL_DRIVER option in the
ANALYZE menu. However, there is a quick way to explore rotational minima using ROT_E from
the ANALYZE option. Read in the equatorial methyl cyclohexane structure and convert one of the
methyl hydrogens to a carbon using the BUILD option from the Draw Tools menu.
After minimization, we will explore the rotational minima of the ethyl group. We will need
to Sel-Atm carbon 1 and the first carbon of the attached
methyl group (carbon 7). If hydrogens obscure these, rotate
the structure until they are not hidden.
Choose Sel-Atm from the tools menu, and click on
the carbon of the ring where the ethyl group is attached and
the first connected carbon atom. One may also use Sel-Bnd
and click on the bond to be rotated. Then select ROT_E
from the ANALYZE menu. Enter an increment of 10 and
an extent of 360. Click on okay (or hit return). The
program will then produce a plot and of energy vs. angle
(this may take a few seconds to appear) similar to that
shown. The energy scale is relative to the energy of the
starting conformation and the angles are in degrees. The
plot can be printed. To return to the structure window: In
the Windows version pull down the File menu and choose
Exit (the plot window has it's own menu bar and under the
File menu there will be two choices, Print and Exit); In the
Macintosh version choose Stick Figure from the View
Menu.
4.4 Benzene and a Pi Calculation
Select DRAW from the TOOLS menu and draw a
hexagon. Next select ADD_B from the TOOLS menu to
change every other bond in the ring to a double bond, by
clicking in the middle of the bonds. Finally, use H/AD to add the hydrogens to create benzene.
Although the structure now looks like benzene, it is not ready to be minimized because PCMODEL
does not have any information about the pi system. Choose PIATOMS from the MARK menu, and
the structure will be redrawn with small ~ symbols near each of the pi atoms. (PCMODEL
automatically determines which atoms are pi atoms, once it has been told to look for them.)
Minimize the molecule using MINIMIZE from the ANALYZE menu, then save it to disk using the
SAVE command from the FILE menu.
4.5 Biphenyl and a Pi Calculation
Begin with the benzene structure studied above as the active structure. Select READ from
the SUBSTR menu, and read the benzene file back into the program. There will now be 2 benzene
rings on the screen, side by side and several inches apart. Sel-Atm one hydrogen from each
substructure, then choose CONNECT from the SUBSTR menu. The screen will be redrawn with
the two hydrogens removed and a carbon-carbon bond in their place. Use Sel-Atm from the
32
TOOLS menu to highlight 4 carbons involved in the biphenyl dihedral, then select
ROTATE_BOND from the TOOLS menu. Change the dihedral angle to plus or minus 5 degrees,
then click on EXIT to return to the main window. Finally, select PIATOMS from the MARK menu
since the atoms in the substructure may not be labeled as pi atoms at this time.
Now minimize the system by choosing MINIMIZE from the ANALYZE menu. This time
all the pi atoms will not lie in one plane. The structure should minimize to a dihedral angle of
about 39 degrees with a shallow potential energy surface.
4.6 Ferrocene - Using Metals and Coordination
The sandwich complex of iron and two cyclopentadiene rings can easily be modeled with
PCMODEL. There are two ways to represent the cyclopentadiene rings: as aromatic rings with two
double bonds and a carbon anion, or as a ring of aromatic carbons. Since the first option would
require a pi calculation, the second option will be used. This atom type is designed to reproduce
the bond lengths and angles of aromatic rings without requiring a special pi calculation.
To begin, draw a five-membered ring. Double bonds may be added, but this is not
necessary when the aromatic carbon type is used. Use the PT (Periodic Table) option from the
TOOLS menu and replace all the ring atoms with atom type Ca (aromatic Carbon). Use H/AD to
add hydrogens, then rotate the ring onto its side using the DIALS box (accessed via the
CONTROL_PANEL option on the VIEW menu). Save the ring to a file, then read it back in as a
new substructure using the READ option in the SUBSTR menu. If the two rings are too close
together, Sel-Atm an atom in one and use SUBSTR MOVE to separate them. Select DRAW and
place an atom between the two rings. To make this the iron atom select METALS, click on Fe and
click on the isolated atom. Select UPDATE to clean up the structure. There should only be one
hydrogen on each of the aromatic carbons, whether or not you have drawn in the double bonds in
the cyclopentadiene rings.
At this time PCMODEL does not know anything about the interaction of the
cyclopentadiene rings with the iron atom. Use Sel-Atm to mark the iron atom and all 10 of the Ca
atoms, then select METAL_COORD from the MARK menu. A dialog box will appear asking for
information about the metal. Since this is an 18 electron complex select "saturated_18_e" for the
electron count. Clicking on OK causes the screen to be redrawn with the metal coordination bonds
shown in red. The structure can now be minimized. If the structure had been minimized without
coordinating the iron to the rings, the iron atom would not have been bonded to anything and would
have wandered out of the picture.
4.7 The Methanol dimer - Hydrogen Bonding and Docking
This calculation will demonstrate the hydrogen bonding and docking capabilities of
PCMODEL. To begin, draw and minimizing methanol. Select DRAW from the TOOLS menu and
draw a 3-carbon skeleton. Next select PT and change the central atom to an oxygen (O) and one of
the terminal carbons to a hydrogen (H). Now use H/AD to add the remaining hydrogens and lone
pairs. If you repeat the H/AD command you will note that the hydroxyl hydrogen is not removed.
Hydrogens attached to heteroatoms are not removed by H/AD and must be removed explicitly
using the DEL command. (This is to ensure that particular hydrogen bonding orientations drawn
by the user will not be disturbed by the normal H/AD function.) Minimize this structure
33
(MINIMIZE on the ANALYZE menu) and then save it in to file (SAVE under the FILE menu).
Since there are no other heteroatoms present, hydrogen bonding was not important during this step.
Next, read the methanol structure back in as a substructure using the READ command
under the SUBST menu. A red line will appear between one lone pair and one hydroxyl hydrogen,
indicating a potential hydrogen bond. Use the MOVE command under SUBST to move the second
methanol molecule around so that the O-H-O system is linear, and is within bonding distance. (By
default Hydrogen bonding is now turned on, use the REST option in the Mark Menu to turn it off).
MINIMIZE (ANALYZE menu) the dimer. If the linear dimer is obtained, the energy should be -3
to -4 kcal. Next select DOCK from the ANALYZE menu to begin a simulated annealing
calculation. The default settings are adequate for this system. Click on OK, and then enter a
filename to store the results of the calculation. If the calculation is successful, the dimer energy
will be between -4 and -5 kcal, and a linear hydrogen bond will be present. The calculation may be
stopped at any point by hitting the ESC key.
4.8 Substructures - Creation and Manipulation
In this example, we will create, move, rotate, hide and reset substructures. First, sketch two
separate structures - a hexane and a pentane. To make the pentane into a substructure, choose SelAtm from the TOOLS menu and click on any atom in pentane. Select CREATE from the SUBST
menu. A dialog box will appear asking for the name of this substructure, type "pentane" and select
OK or hit return. Select LABELS from the VIEW menu and click on "Substructure Numbers".
The atoms will now be labeled with numbers, according to the substructure to which they belong.
Select MOVE from the SUBST menu, and the DIALS box will appear. Since an atom in
the pentane substructure was still selected when SUBSTR MOVE was selected, the DIALS box
will only move the pentane substructure. Click on EXIT to dismiss the DIALS box, then click on
Sel-Atm on the TOOLS menu to de-select all atoms. Now select MOVE from the SUBSTR menu,
and a dialog box will appear with a list of all currently defined substructures. Select a substructure
from this list, and a new DIALS box will appear which will move only that substructure. To move a
different substructure select click on one atom in a different substructure. As long as no other
Draw Tools options have been used, the Sel-Atm option will still be active. This substructure now
becomes the active structure and will be translated or rotated by the DIALS box.
Now click on H/AD to add the hydrogen atoms. Use Sel-Atm to mark one hydrogen in
each substructure, and select CONNECT from the SUBSTR menu. A bond connecting the two
substructures will replace the hydrogens. Select MOVE from the SUBSTR menu, translate one
structure, and notice that the central bond of the hexane is stretched. This will be the case
whenever two separate substructures, which are directly bonded, are moved.
Choose HIDE from the SUBST menu, if no atoms are selected a substructure list window
will appear again. However, each substructure will have a lowercase "v" next to it, indicating that it
is currently visible on the screen. Select pentane and say okay. The pentane structure will
disappear from the display. Select HIDE from the SUBST menu again, and this time pentane will
have an "i" next to it, indicating that it is invisible. Select pentane again and click on OK, and
pentane will re-appear on the screen.
Select ERASE from the SUBSTR menu, and select "Str 0" from the list. Note that the
entire complex is erased. This is because pentane is still part of "Str 0", the initial structure, as well
as being its own substructure ("pentane").
34
4.8.1 Building Polystryene using Dummy Atoms
Read in benzene from the Rings Templates and then select BUILD from the DrawTools.
Select one of the hydrogen atoms on the ring to replace it with a methyl group. Next select one of
the hydrogens of the methyl group and you should now have ethyl benzene. Minimize the structure
to obtain a reasonable geometry. Bring up the Periodic Table from the DrawTools menu and select
the dummy atom type, DU, from the dialog box. Next point to one of the hydrogens of the CH2
group and then the hydrogen anti to the first hydrogen on the CH3 group. Do an HAD sequence
and notice that the hydrogens that were converted to dummy atoms are not removed by the
hydrogen delete. Once the hydrogens are readded do a Minimization. Next , using SUBSTR
READ, read in the pcmod.bak file. Highlight the Dummy atoms by using the Show Dummy
command from the SUBSTR menu. There should be four dummy atoms showing on the screen.
Next select the Connect command from the
SUBSTR menu. This will bring up the
Connect dialog box with the dummy atoms
boxes filled. Selecting Connect will connect
the two structures from the second dummy
atom of structure 1 to the first dummy atom
of structure 2. Selecting Next Structure brings
up a File Open dialog box and a new structure
can be read. Reread pcmod.bak and note that
the Substructure Connect dialog box will be
updated with new atom numbers for the
dummy atoms. Selecting Connect adds the
new structure to the old structure. Repetition
of this procedure makes it easy to build oliogmers. You are not limited to single monomers since
any structure can be read using the Next Structure button. As long as the new structure has two
atoms marked as Dummy Atoms, the substructure connect function will work.
4.9 Diels-Alder Transition State
To model the Diels-Alder transition state for the reaction of butadiene and ethylene, begin
by drawing a hexagon of atoms (a flat cyclohexane). Use PT from the TOOLS menu to replace
atoms 1 and 2 by C* and atoms 3 and 4 by C# and atoms 5 and 6 by C•. Use H/AD to add
hydrogens and select MINIMIZE from the ANALYZE menu to optimize the structure. A dialog
box will appear inquiring about what bond orders to use. The C*-C* bond represents a sigma bond
being formed between one terminus of butadiene and one terminus of ethylene. Enter 0.3 for this
bond order. The C#-C# bond represents the other sigma bond being formed. Enter 0.3 for this
bond also, and then click on OK. This will start the minimization. The resulting structure should
be very similar to that calculated by Houk et al. (Houk, K. N., Paddon-Row, M. N., Rondan, N. G.,
Wu, Y. D., Brown, F. K., Spellmaeyer, D. C., Metz, J. T., Li, Y., and Loncharich, R. J. Science,
1986, 231, 1108 and references therein.)
35
It should be noted that the bond length between the two C• carbons is 1.4 Å. (You can
check this by selecting QUERY from the TOOLS menu, then clicking on each of the C atoms, then
on a blank space on the screen. The distance between the two atoms will be displayed on the
screen. To remove the distance from the screen, click on UPDATE twice.) If a normal double
bond were drawn between these two atoms, the resulting minimized structure would have a 1.34 Å
bond between these two carbons, which will ultimately give a double bond in the product.
If other bond orders are chosen, the distances between the C* or C# carbon pairs will
respond, as will the 1,3 angles at C* and C#. The calculated MMX energy is the potential energy
of the system relative to the potential functions for the transition state, NOT relative to the ground
state. As usual, the potential energy of a minimized structure can only be compared to a
conformational isomer or a diastereomer. The potential energy of a transition state with one set of
bond orders might be compared to the potential energy of another transition state with different
bond orders, but only the difference in steric energy can be determined, not the actual free energy
difference between the two structures. That is, the electronic energy difference is not considered in
the MMX calculation. See the chapter on the MMX force field for more information.
36
37
Chapter 5. Drawing Tools
The palette of drawing tools appears at the left-hand side of the drawing window
when PCMODEL program is started. The palette can be moved anywhere on the screen
by dragging on the "Tools" title. The window can be closed by clicking on the
CANCEL button at the very bottom, and recalled by selecting DRAW from the EDIT
menu.
5.1.1 Select Atom
This option allows certain atoms to be selected for action by future commands.
As many atoms as desired can be selected. To clear all selected atoms, click again on the
SELATM button
5.1.2 Select Bond
This option allows bonds to be selected for action by future commands. As many
bonds as desired can be selected. To clear all selected bonds, click again on the
SELBND button
5.2 Draw
This command enables the drawing mode. To create a new structure, select
DRAW then move the cursor to the desired location and click the left mouse button. If
the cursor is then moved to a new location and the left mouse button is clicked again, a
line will be drawn, indicating a bond between the previous atom and the new one just
placed. If the cursor is moved to a new location and the left button is clicked again, a third atom
will be created and bonded to the second atom. Note that all atoms are added in the plane of the
screen.
To close a ring, place the cursor on an existing atom and click the button. The cursor must
be within about 1/4 inch of an atom to draw a bond to that atom instead of creating a new one. A
small box will appear around the atom when the cursor is close enough. To start drawing from an
existing atom without adding a new bond to that atom, click on DRAW again, place the cursor on
the old atom, click and continue drawing as before. New atoms will be added in the same plane as
the last atom picked. To start drawing from a new location, click on the DRAW button again then
move to the new location and click the mouse. A small dot will appear indicating a new atom.
Clicking on DRAW, then selecting first one end of the double bond, then selecting the other
end may create double and triple bonds. Conventional double lines will be used when the structure
is redrawn. Alternatively, the ADD_B option can be used (see below). If there are many multiple
bonds, this is the easier method to use.
5.3 Build
This option allows for rapid building of 3-D structures. After selecting BUILD, click on
any hydrogen and it will be replaced with a methyl group. This option allows PCMODEL to
provide the 3-D information required to build the structure, as opposed to the DRAW option, where
all atoms are added in the plane of the atom to which they are connected. (Or, in the plane of the
screen, in the case of unattached atoms.) The structure may be rotated and viewed with tubular
bonds to get a better 3-D view of the molecule. The Stick Figure view is best for selecting atoms.
When building rings the ring closure bond can be generated by selecting the two atoms and then
Add_B.
5.4 Update
This option redraws the screen, and updates the structure with any changes since it was last
drawn. It clears any Query information.
5.5 H/AD
This command will automatically add or delete hydrogens and lone pairs. The structure
will be redrawn with the appropriate structure. Hydrogens and lone pairs attached directly to metals
will not be removed. Hydrogens attached to oxygen and nitrogen are not removed to preserve the
orientation of hydrogen bonds.
Note that removal of hydrogens followed by re-addition will not necessarily return you to
the original structure. Hydrogens are added according to a geometric prescription. To remove
hydrogens for viewing or comparison purposes only, use the H/OO command (see below).
5.6 Add_B
This command increments the value of the selected bond by one (single to double to triple).
After selecting ADD_B, click in the center of the bond to be incremented. An X will appear over
the bond when you are close enough. The structure will be redrawn with the conventional double
or triple line representation. If there are two atoms selected then Add_B will make a bond between
the selected atoms. This is useful for closing rings generated by Build.
5.7 In
This command pushes selected atoms behind the plane of the screen, by approximately 0.33
Å. Each time an atom is clicked on it will be pushed in an addition increment.
5.8 Out
This command pulls selected atoms out of the plane of the screen, by approximately 0.33 Å.
Each time an atom is clicked on it will be pulled out an addition increment.
39
5.9 Del
This command DELetes an atom or bond. After selecting DEL, click once on each atom or
bond to be deleted and the structure will be redrawn with the atom or bond deleted. If an atom is
deleted, all bonds to that atom are deleted, as well as any attached atoms. Thus, you only need to
click on the carbon to delete an entire methyl group. It is important to do an H/AD command
before writing a file if any atoms or bonds were deleted. This ensures that any "holes" created but
not removed from the arrays will be removed during this process and that the heavy atoms will be
in the proper sequence.
5.10 Move
This command moves an atom into a new position. After selecting MOVE click on the
atom to be moved, then click in the new position. The structure is redrawn the atom will be moved.
Multiple MOVEs may be done at one time, until another option is chosen.
5.11 Rotate Bond
This command rotates the central bond of the four selected atoms. Use SELATM to first
select the four atoms. The selected atoms will be marked by small gray dots.
5.12 Query
This command is used to measure atom positions and charges. POAV, bond lengths, angles
and dihedrals. To determine the position and charge of an atom, or obtain the POAV, select
QUERY click on an atom and then a blank space on the screen. To measure a distance, select
QUERY, click on the two atoms whose distance is to be measured, then click on a blank area of the
screen. The distance between the two atoms will be displayed on the screen at the location of the
last click. To measure an angle, click on the three atoms forming the angle of interest, then a blank
area of the screen. The numerical value of the angle will be displayed. Similarly, to measure a
torsion angle click on the 4 atoms of the torsion then a blank area. If you select two vicinal
hydrogens or if you select four atoms of a dihedral and the first and last atoms are hydrogens the
PMR coupling constant will be calculated. The PMR coupling constants are corrected for
electronegativity according to the method of Haasnoot, DeLeeuw and Altona, Tetrahedron 1980,
36, 2783.
Any number and combination of distances, angles and torsion angles may be measured,
until another option is chosen. The queries can be printed and will remain on the screen during
minimization and dynamics calculations so that changes in the structure can be monitored. To clear
the values from the screen, click on UPDATE twice.
40
5.13 PT
This command calls up a window containing a list of atom
types. An atom may be changed to a different type by selecting the
new type from the Periodic Table window, then clicking on the atom
to be changed. Multiple atoms may be changed to the same type
without re-selecting the type. A complete listing of atom types is
given in the MMX Force Field chapter. Clicking on CANCEL closes
this window.
5.14 Metals
This command calls up a window
containing a list of metal atom types. An
atom may be changed to a particular metal by
selecting the appropriate metal from the list,
then clicking on the atom to be changed. The
electron count (saturated, unsaturated, high
spin, low spin or square planar), charge and
coordination of a metal to a pi system are set
with the Metal Coord menu item in the Mark Menu. Clicking on CANCEL closes this window.
41
5.15 Rings
This command calls up
a window containing a list of
ring templates. A complete
listing of the rings is given in
Appendix B. Selecting a ring
from the list causes that
structure to be placed in the
structure window as a new
substructure. Clicking on
CANCEL closes this window.
5.16 AA
This command opens a
dialog box containing 24
standard amino acid residues.
Selecting one of the amino
acids causes that structure to be
drawn in the structure window.
If the CONNECT box is
selected, the secondary
structure of the connection
(alpha helix, beta sheet, beta
turn type I or beta turn type II) must be specified prior to selecting the amino acid sequence.
Clicking on CANCEL dismisses this window. A complete list of all the amino acids is given in
Appendix B.
5.17 Su
42
This command
opens a dialog box
containing 25 standard
sugar residues.
Selecting one of the
names causes the
corresponding structure
to be drawn in the
structure window. If the
CONNECT box is
checked, the structure of
the connection (alpha or
beta) must be specified prior to selecting the sequence. Clicking on CANCEL dismisses this
window. A complete listing of all the sugars is given in Appendix B.
5.18 Nu
This command opens a dialog box containing
5 nucleosides. Selecting one of the names causes the
corresponding structure to be drawn in the structure
window. The default is to draw DNA, but clicking on
the RNA button instead may draw RNA. If the
CONNECT box is checked then a letter symbol
representing the Nucleoside chosen will be written in
the edit box. When all the nucleosides are entered selecting Build will generate a single strand of
DNA or RNA. Selecting Build Double will build a double strand. Clicking on CANCEL dismisses
this window. A complete listing of all the nucleosides is given in Appendix B.
5.18 Organo Metallics Templates
This command calls up a window containing a list of organometallic templates. These are
structures that have been built and saved in a file. Selecting a structure from the list causes that
structure to be placed in the structure window as a new substructure, which can then serve as the
starting point for building new structures. Clicking on CANCEL closes this window.
43
5.20 Transition State Templates
This command calls up a window containing a list of transition state structures. These are
structures that have been built and saved in a file. Selecting a structure from the list causes that
structure to be placed in the structure window as a new substructure, which can then serve as the
starting point for building new structures Clicking on CANCEL closes this window.
44
45
Chapter 6. Conformational Searching
GLOBAL-MMX (GMMX) is a steric energy minimization program which uses
the currently selected force field to search for the global energy minimum and other low
energy local minima. Processing by GMMX is done in two stages. The first stages
randomly searches over the selected rings and rotatable bonds and keeps all conformers
within 3.5 Kcal of the lowest energy conformer found (Eminim) during the minimization.
The second cycle reminimizes the structures found in the first cycle and keeps only those
which are within 3.0 Kcal of the lowest energy conformer. The default energy windows
for the two cycles can be changed. In addition to an output file containing the
coordinates of the final structures, a textual summary file called
'<OUTPUT_FILENAME>.pkm' is produced which lists the energy and Boltzmann
distribution of each low energy conformation. This file may also include a listing of
query operations (PMR coupling constants, distances, angles, and dihedrals) for each
structure as well as a Boltzmann averaged summary.
Although the conformational searching techniques that follow are unique in their
approach, the methods described by the Still group (see M. Saunders, K.N. Houk, Y-D
Wu, W.C. Still, M. Lipton, G. Chang, and W. Guida J. Am. Chem. Soc. 112, 1419 (1990)
and references to previous work cited there in.) were the inspirational source for this
work. The search techniques in GMMX are based on the methods used in BAKMDL,
developed by Professor Kosta Steliou of Boston University, and ported to the MMX force
field by Mark Midland of UC Riverside and Joe Gajewski and Kevin Gilbert of Indiana
University. We wish to thank Professors Still and Steliou for sharing with us
unpublished work and code that greatly enhanced our routines.
Conformational space can be
searched by GMMX in three ways.
These are the Mixed method, the
Bonds method and the Cartesian
method. The Bonds method
randomly selects a subset of the
bonds designated by the user for
rotation. Bond rotation can cause
large changes in the shape of a
molecule. The Cartesian method
randomly moves a subset of all
heavy and nonvolatile atoms in 3d
space causing small changes in the
shape of the molecule. The Mixed
method alternates between the
Bonds and Cartesian methods and is
the preferred method. This
procedure is especially efficient with
46
cyclic structures having side chains. You may select ring bonds for rotation as well as the side
chain bonds but restricting the bond selection to the side chain bonds usually is all that is
necessary if only 3 to 7 member rings are present. The coordinate (Cartesians) movements will
apply to the entire structure.
When GMMX is first selected from the Analyze Menu a dialog box will be presented as
shown above. This dialog box controls the setup and running of GMMX. Items that can be set
directly in this dialog include the jobname, the search method (bonds, coordinates or both
(default)), and the energy windows for the first and second cycles. The buttons Setup Rings,
Setup Bonds, Comparison Method, Setup Queries, Options, and Read Job all call up further
dialog boxes to setup the various options. Save Job allows the user to save a file of the current
GMMX options, and Read Job reads this file. Run GMMX starts the first cycle processing while
Run 2nd Cycle starts the job in the second cycle, which presumes that a file of structures saved
from the first cycle is available.
6.1 Setup Rings
GMMX will automatically search for all rings in the current structure and the results will
be listed in a scrolling list
window. To search on a
particular ring select that
ring from the list of rings
and the select the Add
button. In molecules
containing fused or
multicyclic ring systems all
possible permutations of
the rings will be listed.
Thus trans decalin will
have entries for two six
membered rings and one
ten membered ring. Care
should be taken in selecting
the correct ring entry to
search. During the search
the ring will be broken
between the first two atoms
of the Atom Number list.
These are displayed as
Closure Atom 1 and 2. The
Closure Atoms may be edited but they must be adjacent atoms.
47
6.2 Setup Bonds
To designate rotatable bonds select the Setup Bonds option in the dialog box. A new
dialog box will be shown. The atom numbers of the
rotatable bond can be entered in the edit boxes. When
the ADD button is selected the atom numbers are read
and checked to see that a bond exists between the two
atoms. If a bond is found then the default rotation
increment for this bond is then determined and the
bond is added to the scrolling list of bonds for
searching. Bonds may also be entered by using SelBnd from the Draw Tools. To use this option, select
the bonds before bringing up the Setup Bonds dialog
box. The selection may be done while the main
GMMX dialog box is up. Just move the box to the
side and rotate and select the bonds. When Setup
Bonds is selected, the selected bonds will appear in the
scroll list. To delete a bond, select the bond from the
scrolling list and then select Delete.
Bond Resolution
If the bond is an ester or an amide, the resolution set will have two angles (0 and 180
degrees). If the bond is an SP3-SP3 bond, then three angles are used (0, 120, and 240 degrees).
If the bond is SP3-SP2, twelve angles are considered (0, 30, 60, 90, 120, 150, 180, 210, 240, 270,
300, and 330). If the bond is SP2-SP2, 6 angles are chosen (0, 60, 120, 180, 240, and 300).
Finally, if the bond is a ring bond, then if the ring is 10 atoms or less, the resolution set will have
12 angles of 30-degree increments as above and if it is 11 atoms or more, 6 angles of 60-degree
increments will be used. The user can override these default settings (except for no-rotatable
bonds) and enter their own values.
Additional Ring Information
For each ring defined, GMMX will calculate closure angles and a closure window.
Again, the user can accept these values or enter others. Within GMMX each bond is randomly
rotated by each angle in the resolution set. The newly created geometry is then analyzed to see if
each ring can be reclosed within the defined limits of closure. It is checked for bad 1,5 C-C
VDW interactions and trans annular interactions. Structures with up to 2 additional bad 1,5 CC VDW interactions beyond the original structure may be kept. The structure is also screened
for epimerizations and all other constraint criteria such as distances, dihedral angles etc. imposed
during the interactive procedure. If all the constraint criteria are satisfied, the conformer is
processed by GMMX.
6.3 Setup Query
The Setup Queries dialog box allows one to
specify query information for the second cycle.
Clicking on the four options will bring up dialog
48
boxes for entering atom numbers. For distances the atom numbers must be entered in sets of 2,
for angles sets of 3, for dihedrals sets of 4 and for coupling constants sets of 2. This process may
be automated by performing the query on the structure on the screen. This may be done prior to
setting up GMMX or while the main GMMX dialog box is on the screen. Use Query on the
Draw Tools. When one of the four options is selected, the query information will appear in a
scroll list. The final output file, jobname2.pkm, will contain a list of the queries for each
structure as well as a summary total based on a Boltzmann average.
6.4 Comparison Method
The Comparison Method dialog box allows one to
choose various options for structural comparisons during the
search. The default is to compare all nonvolatile atoms.
Nonvolatile atoms are those that are not removed in an
H/AD operation, i.e. all heavy atoms and hydrogens on O or
N. The equivalent atoms and Specific Sequence options
have not yet been implemented. Numerical isomers are
found in unsubstituted rings such as cyclooctane. Reflection
isomers are found in unsubstituted acyclic compounds such
as butane. A set of specific atoms may be compared by
clicking the Specific non-volatile atoms box and entering a
set of numbers in the edit box. The default comparison
routine uses a fast analytical method during the first cycle
and a slower but more accurate method during the second
run. It is usually better to err on the side of over collecting
on the first run and then weed out duplicates on the second
run.
49
6.5 Options
The Options dialog box allows one to
change several options for the search. Chirality will
be checked and enantiomers rejected if the box is
checked. Hydrogen bonding will be on by default.
If the system has pi atoms turned on, a pi
calculation will be performed. Note that this may
not be necessary and may require more time for
rigid systems like benzene. By default, structures
will be screened for bad 1,5 interactions and
rejected if found prior to minimization.
Conformational enantiomers such as the two gauche
forms of butane will be kept. An early bail out of
the minimization can be done. This applies a
sliding high energy cut off of 5-15 kcal/mol above
the minimum energy found to the structure during
the 50-100 iterations of the first-derivative
minimization. If the structure is 15+ kcal/mol
above the lowest energy structure at the 50th
iteration, it will be rejected and the search will
move on. This cut off is not used during the second
cycle. This method may lead to premature bail out
if there are a lot of hydrogen bonds in the structure.
The structures will be sorted by energy. The option
to sort by heat of formation has not been implemented. The Boltzmann temperature is used to
calculate the distribution of isomers. The cutoff distance and energy are used during structure
comparisons. During both cycles all structures within 0.25 kcal/mol of the current structure will
be examined. During the first cycle a structure will be considered to be unique if any atom is
more than 0.25 Angstroms away for the least squares fit. In the second cycle the RMS average
must be greater than 0.25 Angstroms. The random number generator uses the seed value. A
search starting with the same starting structure will always follow the same path unless the seed
value is changed. The search will stop after the lowest energy structure (emin) has been found 5
times or there are 25 duplicates in a row without a new structure. However at least 50 structures
must be minimized. The default number of duplicates required is 2.5 times the number of heavy
atoms with a maximum of 50. The search will also stop if 100,000 structures have been
minimized.
6.6 Run GMMX
Once all the setup is done GMMX can be run. In all methods the original structure is
minimized to generate the initial minimum energy conformation. The structure is then modified
by either the bonds or Cartesian method and the new conformation is checked for bad-1, 5
50
interaction, and epimerization. If all the acceptance criteria are satisfied, the structure is
minimized. If the minimization yields an energy acceptable conformer that HAS NOT BEEN
FOUND BEFORE, it is saved and its geometry is used to spawn a new conformer, otherwise, it
is rejected. Only accepted conformers are permitted to carry-on the search. If attempts to create
a new conformer fail, based on the acceptance criteria, it is sent back to try again until a NEW
ACCEPTABLE conformer is created. Statistical searching on coordinates should be selected
whenever a rigid or fused polycyclic system is to be analyzed. If there are side chains then the
Mixed procedure should be favored. The Bonds method is best for acyclic structures.
6.7 Run 2nd Cycle
Run GMMX will automatically run the first and second cycle of the search. The second
cycle refines the structures found in the first cycle by throwing out unnecessary duplicates and
cutting down the energy window. It also performs any Query operations. The structure output
files from both searches are kept. You can send the search output through the second cycle at a
later time by using this option. The run will use any criteria (such as Query information) which
you have selected.
6.8 Save Job
This option will bring up a file-save dialog box. The default file name will be the Job
Name entered in the GMMX dialog box. The file save will save <JobName>.pcm and
<JobName>.inp files. The inp file contains the name of the pcm structure file and the directions
for doing the search. Thus the pcm file cannot be deleted or renamed if you wish to run this job
later. The inp file may be read by the DOS or text-based version of GMMX.
6.9 Read Job
This option brings up a file read dialog box and reads the inp file saved in Save Job. All
options will be updated to the settings in the job file
51
52
Chapter 7. File Menu
This menu contains the following commands:
Open
Save
Save Graphic
Save Movie
Print
Read pcmod.bak
Exit
Reads a file containing a molecular system
Writes a molecular system to a file
Writes a file containing a picture of the screen
Writes a file containing a Movie
Print the current molecular system
Read the structure backup file
Exit PCMODEL
7.1 Open
The OPEN option in the FILE menu is used to read a new structure file into
PCMODEL. Any structure on the screen will be erased.
Macintosh: Selecting OPEN immediately brings up a standard Macintosh file
open dialog box with the different file formats listed in a drop down window at the
bottom of the dialog box.
Windows and Linux: Selecting OPEN immediately brings up a standard Windows
Open File dialog box which gives the current path, an edit window for the filename, a
drop down box containing the various file types supported by PCMODEL, a window
53
listing directories and disk drives, and a scrollable window listing the files in the current
path (if a wildcard expression is used for the filename). When the dialog box first
appears, the PCMODEL file type is selected and all files with the .pcm file extension will
be shown. A filename may be entered by typing the name in the filename edit box or by
selecting (with the mouse) a file from the scrollable file list box. To see files available in
the current path, use a wildcard expression such as *.PCM to see all files with the PCM
extension, or *.* to see all files.
PCMODEL supports several different types of files. Clicking on the combo box
at the bottom of the dialog box will show all the types of files that can be read in
PCMODEL. The default file type is PCMODEL.
File Types Read by PCMODEL
PCMODEL files contain information about all the atoms and bonds in a molecule,
including information about hydrogen bonding, pi atoms, metal coordination and
substructure membership. It is the most general file type for molecular mechanics
information, is a free format ASCII text file, and can be read or edited with any word
processor. A PCMODEL file can contain either one structure or multiple structures.
PCMODEL files can be read by Gaussian 92 and can serve as input to this ab initio
quantum chemistry program. (A full description of this file type is given in chapter 16.)
MMX files are essentially MMP2 formatted files (see QCPE program number 395 for a
detailed description). These files contain information about atoms and bonds in a
molecule, including information about pi atoms, hydrogen bonding and metal
coordination, but not substructure membership. An MMX file can contain either one
substructure or multiple substructures. It is an ASCII text file with a fixed, Fortran
format, and can be read or edited with any word processor. The fact that it is fixed
format means that data must be entered in specific columns to be read correctly, which
makes editing difficult. (A full description of this file type is given in chapter 16.)
MM3 files contain information about all the atoms and bonds in a molecule written in the
MM3 format and using MM3 atom type rules. MM3 files are text files and use a Fortran
type fixed format. The files may be edited with a text processor, but the fixed format
requires that data be entered in specific columns to be read correctly.
PDB files are structure files using the Protein Data Bank format developed at
Brookhaven National Laboratory. The PDB format can be used to describe any molecule
and is not restricted to proteins or nucleic acids. The PDB format contains information
about the atom type, the residue name if part of a protein or nucleic acid, and the atomic
coordinates of the atom. Bonding information may be included in the file but it is not
required. PCMODEL reads PDB files and tries to determine the bonding arrangement
based on internuclear distances. While this method is good it is not perfect and the bonds
shown when a PDB file is read should be looked at carefully before further calculations
are attempted.
54
MOPAC INP and ARChive files are used by the semi-empirical quantum chemistry
programs, AMPAC and MOPAC (QCPE program number 514). These files contain a list
of atom symbols, bond lengths, angles and dihedral angles, but no information about
bonding. MOPAC files may be used for input to the AMPAC, MOPAC and Gaussian
programs since all of these programs can read and interpret internal coordinates. The INP
file is an input file to AMPAC or MOPAC in Z matrix format and the ARChive file is the
archive output file written by Mopac (normally FOR012) and contains the optimized
geometry in Z matrix form and the atomic charges calculated by Mopac. Both the
structure and charges can be read into PCMODEL.
Alchemy and Sybyl molecular modeling programs marketed by Tripos Associates (St.
Louis, MO) use ALCHEMY and SYBYL files. Alchemy file format is also used by
Chemical Abstracts Service for 3D-structure information.
MACROMODEL files are molecular mechanics type files generated by the Macromodel
program. This large molecule modeling program, developed by C. Still, Columbia
University, runs on workstations and provides many facilities for handling large
molecules. Macromodel files contain information about atoms and bonds, but no
information about pi atoms, hydrogen bonding or transition metals.
X-RAY files are free format structure files in a format that has been developed for
reading x-ray crystal data. X-ray structure files only contain information about atom
types and positions. (A full description of this file type is given in chapter 16.)
CHEM-3D is a molecular modeling program developed by Cambridge Scientific
Software for use on a Macintosh computer. PCMODEL reads and writes the Cartesian
type II structures. Chem-3D can be used to generate publication ball and stick pictures.
TINKER is a molecular modeling program developed by Professor Jay Ponder of
Washington University ([email protected]). PCMODEL reads and writes the xyz
cartesian filetype.
MDL_MOL files are structure information files in the molfile format developed
by MDL Information Systems Inc. Molfiles can be generated by programs such as
Isis™ Draw, or as the result of a search of the REACCS or MACCS databases.
Molfiles contain 3-D structure and bonding information.
SDF are structure files generated by the structure building programs Corina and Concord
and can also be output by Isis Draw (as 2D files).
Gaussian files are the output files (text) written by the Gaussian Quantum
Chemistry programs running under Windows, on a workstation or supercomputer.
Since PCMODEL reads the text file, the output file is portable across all these
platforms.
55
Gaussian ChkPt files are the formatted checkpoint files generated by the
Formchk utility of the Gaussian program.
Jaguar Input and Log files are input and output files written by the Jaguar quantum
chemistry program from Schrodinger, Inc.
CSSTR files are Cambridge Structural Database files.
Gamess files are the output files (text) written by the Gamess Quantum
Chemistry programs running under Windows, Macintosh, on a workstation or
supercomputer. Since PCMODEL reads the text file, the output file is portable
across all these platforms.
Hondo files are the output files (text) written by the Hondo Quantum Chemistry
program. Since PCMODEL reads the text file, the output file is portable across
all platforms.
ADF files are the output files (text) written by the Amsterdam Density Functional
quantum chemistry program. Since PCMODEL reads the text file, the output file
is portable across all platforms.
Turbomole files are the output files (text) written by the Turbomole quantum
chemistry program. Since PCMODEL reads the text file, the output file is
portable across all platforms.
PQS files are the output files (text) written by the Parallel Quantum Systems
(PQS) quantum chemistry program. Since PCMODEL reads the text file, the
output file is portable across all platforms.
Smiles strings are a linear, 1D, notation for chemical structures. Pcmodel reads
the string and attempts to build a 3D structure based solely on the atom types and
connectivity.
7.2 Save
The SAVE option is used to write the current molecular system to a disk file.
Macintosh: Selecting Save brings up a dialog box listing the current types of files
PCMODEL can write. Select the appropriate file format and then OK. The standard
Macintosh file save dialog box will then be presented.
Windows and Linux: Selecting SAVE brings up a standard Windows File Save
dialog box which gives the current path, an edit window for the filename, a list box
containing the various file types supported by PCMODEL, a window listing directories
and disk drives, and a scrollable window listing the files in the current path (if a wildcard
expression is used for the filename). All files with the default extension will be shown.
56
The last file name used will be retained. If this file is used again, you will be asked if you
want to replace the file or append the structure onto the existing file.
When the dialog box first appears, a wildcard expression is displayed in the
filename edit box, and the PCMODEL file type is selected. All files that match the
wildcard expression will be listed in the file list box. A filename may be entered by
typing the name in the filename edit box or by selecting (with the mouse) a file from the
scrollable file list box. To see files available in the current path, use a wildcard
expression such as *.PCM to see all files with the PCM extension, or *.* to see all files.
If the filename that is entered already exists, a dialog box will appear asking if the
new structure is to be appended to the existing file, or if the existing file is to be replaced.
Choosing APPEND to generate multiple structure files or libraries of related structures.
The current directory is given in the current path box. The directory list box
displays all directories below the current directory, the directory one level up from the
current directory ([..]), and all other disk drives on the computer. The current path may
be changed by selecting either another directory or disk drive in the directory list box.
PCMODEL supports several different types of files. Clicking on the combo box
at the bottom of the dialog box leads to a drop down menu of all the files written by
PCMODEL. The default file type is PCMODEL. MMX atom types are assumed for all
files except MM3 files where the MM3 atom types are assumed.
File Types Written by PCMODEL
PCMODEL files contain information about all the atoms and bonds in a molecule,
including information about hydrogen bonding, pi atoms, metal coordination and
substructure membership. It is the most general file type for molecular mechanics
information, is a free format ASCII text file, and can be read or edited with any word
57
processor. A PCMODEL file can contain either one structure or multiple structures.
PCMODEL files can be read by Gaussian 92 and can serve as input to this ab initio
quantum chemistry program. (A full description of this file type is given in chapter 16.)
MMX files are essentially MMP2 formatted files (see QCPE program number 395 for a
detailed description). These files contain information about atoms and bonds in a
molecule, including information about pi atoms, hydrogen bonding and metal
coordination, but not substructure membership. An MMX file can contain either one
substructure or multiple substructures. It is an ASCII text file with a fixed, Fortran
format, and can be read or edited with any word processor. The fact that it is fixed
format means that data must be entered in specific columns to be read correctly, which
makes editing difficult. (A full description of this file type is given in chapter 16.)
MM3 files contain information about all the atoms and bonds in the molecule. The MM3
atom types are used and pi atom marking is supported.
MOPAC and AMPAC files are used by the semi-empirical quantum chemistry
programs, AMPAC and MOPAC (QCPE program number 514). These files contain a list
of atom symbols, bond lengths, angles and dihedral angles, but no information about
bonding. MOPAC files may be used for input to the AMPAC, MOPAC and Gaussian
programs. The dialog box will facilitate writing the file.
58
ALCHEMY and SYBYL files are used by the Alchemy and Sybyl molecular modeling
programs, marketed by Tripos Associates (St. Louis, MO). Alchemy format is also used
by Chemical Abstracts Service for 3D structure information.
MACROMODEL files are molecular mechanics type files generated by the Macromodel
program. This large molecule modeling program, developed by C. Still, Columbia
University, runs on workstations and provides many facilities for handling large
molecules. Macromodel files contain information about atoms and bonds, but no
information about pi atoms, hydrogen bonding or transition metals.
CHEM-3D is a molecular modeling program developed by Cambridge Scientific
Software for use on a Macintosh computer. Chem-3D can be used to generate
publication ball and stick pictures.
Tinker is a molecular modeling program developed by Professor Jay Ponder of
Washington University in St Louis. PCMODEL generates an xyz cartesian file that can
be read by Tinker.
PDB files contain the Cartesian coordinates of the current structure written in PDB
format.
Jaguar Input files are written for the Jaguar quantum chemistry program. They include
the Cartesian coordinates of the structure and the atomic symbol.
Gaussian Job files are input files for the Gaussian quantum chemistry program.
Structural information can be output in either Cartesian or Z matrix format and many
options may be set using the dialog box. The Keywords section is updated each time an
option is selected. If you wish to add additional keywords not available through the
options, they should be added just before OK is selected.
Gamess input files will bring up a dialog box similar to the Gaussian box.
Hondo input files will bring up a dialog box similar to the Gaussian box.
SDF are structure files generated by the structure building programs Corina and Concord.
ADF files are the input files (text) for the Amsterdam Density Functional
quantum chemistry program Since PCMODEL writes a text file, the file is
Turbomole files are the input files (text) for the Turbomole quantum chemistry
program. Since PCMODEL writes a text file, the file is portable across all
platforms.
59
PQS files are the input files (text) for the Parallel Quantum Systems (PQS)
quantum chemistry program. Since PCMODEL writes a text file, the file is
Smiles strings are a linear, 1D, notation for chemical structures.
7.3 Save Graphic
This option saves the screen in one of the following file formats; GIF, BMP,
HPGL, PostScript or POVRAY. The file may then be imported into other programs for
editing. The POVRAY option will
write a file for input into the rendering
program POVRAY. This program is
freely available for a number of
platforms (PC, Mac, UNIX) at
http://www.povray.org. It will
provide a ray-traced picture of the
molecule as shown to the left for
potassium 18-crown-6.
7.4 Save Movie
Save Movie writes a file in AVI format. The current options are to Rotate the
structure about X, about Y, about Z, about X then Y and Rotate Bond. Any view
of the molecule can be used. This is a method for generating short movie excerpts
for lectures or PowerPoint presentations.
7.5 Print
Print sends the current structure and related information to the default Windows
printer (which may be a file). The Print Manager handles printer selection in WindowsTM
or by the Chooser on the Macintosh. When PRINT is selected, a dialog box appears
containing the currently selected printer. If the current structure is drawn as a stick figure
then a dialog box will be shown with options for printing the current structure and
60
compare or energy windows. If the current structure is drawn in Ball and Stick, Tubes or
CPK modes then the second dialog box will not be shown and the output and compare
windows will not be printed. Any information in the structure window (such are queries)
will be sent to the printer along with the structure.
7.6 Read pcmod.bak
Every time a minimization is started and upon its completion a structure file,
pcmod.bak, is written to the current working directory. This option will read in this file.
7.7 Exit
This option leaves PCMODEL and returns to the operating system. A dialog box
asks for confirmation before exiting. Note that any unsaved work will be lost when
PCMODEL is exited.
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62
Chapter 8 Edit Menu
The EDIT menu contains the following commands:
Draw
Erase
Structure Name
Hide Hydrogens
Epimer
Enantiomer
Remove LP
Retype
Set Atom Type
List Atom Types
Read Pcmod.Out
Read Pcmod.Err
Copy__To_Clipboard
Orient_XY Plane
Orient_XZ Plane
Orient_YZ Plane
Build Solvent Box/Solvate
Build Periodic Box
Recovers the TOOLS menu
Erases all structures
Edit or enter name of current structure
This option toggles display of hydrogen atoms on
and off. The hydrogens are not removed from the
structure, merely un-displayed. This allows for a
much clearer drawing without changing the
geometry as with H/AD.
Epimerizes the selected atom by interchanging the
two selected attachments.
Reflects the structure through a specified axis.
Remove lone pairs from heteroatoms.
Force PCMODEL to retype the current structure.
Sets the atom type of the selected atom
Lists all the atom types in the current force field
Read Pcmod.out into a simple text editor.
Read Pcmod.Err into a simple text editor.
Copies an image of the structure window to the
clipboard.
Orient the molecule in a specified plane, placing
the first selected atom at the origin, the second
atom along the axis and the third atom in the
plane. Useful when generating structures for
MO calculations
Build a box of solvent molecules or solvate the
current structure.
Build a periodic box from the current structure.
8.1 Draw
The DRAW option brings back the Drawing Tools buttons if they are not visible,
or makes them the active window if they are visible. Otherwise, this command does
nothing. The commands in this Tool bar are described in detail in chapter 5 of this
manual.
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8.2 Erase
This command erases the current structure and resets the default conditions for
modeling. Since any unsaved structures will be lost, a dialog box appears and
confirmation is required before the structure is actually erased.
8.3 Structure name
This option brings up a dialog box for entering or editing the name of the current
structure. The default structure name is "untitled". If a file containing a named structure
is read, then the current structure name is replaced by the name from the file. The
structure name is displayed in the title bar of the PCMODEL window, just to the right of
the word "PCMODEL". The structure name is limited to 60 characters and will be
written into the structure file whenever the structure is written to disk (if the filetype
selected supports structure names).
8.4 Hide Hydrogens
This option toggles the display of hydrogens attached to carbon. The atoms are
still present in the structure database they are just not displayed. This will often make the
display less cluttered, especially if atom numbers or types are being displayed.
8.5 Epimer
This option allows for inversion of the stereochemistry at a particular chiral
center. Before selecting EPIMER, the central atom and the two attachments to be
switched must have been selected with the SELECT command from the TOOLS menu.
Once the three involved atoms have been SELECTed, the EPIMER option can be chosen
and the position of the two attachments (and all atoms attached to them) will be
exchanged. This option will not work if the two attachments are connected to each other
in a chain.
8.6 Enatiomer
This option allows for enatiomerization of the structure by reflecting through an
axis selected by the user.
8.7 Remove LP
This option forces immediate removal of lone pairs from heteroatoms. Only the
MMX force field uses lone pairs and lone pairs are normally removed automatically
when calculations are done with any other force field. However, you may force removal
of lone pairs with this option.
8.8 Retype
This option forces PCMODEL to retype the current structure.
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8.9 Set Atom Type
This option allows the user to specify the atom type of the currently selected
atom. This option is often used in conjunction with added parameter files to define new
atom types or to redefine old atom types that are not recognized by the atom type parser.
The selected atom will not be retyped automatically.
8.10 List Atom Types
List all the atom types in the currently selected force field.
8.11 Read Pcmod.out
This option forces PCMODEL to close the output file, Pcmod.out, and read the
file into a text editor. This allows the user to view the output of a calculation without
exiting Pcmodel. If there is an error with missing constants that information will be
written into Pcmod.out. Once the editor is started it can be used to read the appropriate
parameter file to add the missing constants.
.
8.12 Read Pcmod.err
This option forces PCMODEL to close the error file, Pcmod.err, and read the file
into a text editor. If there is an error with missing constants that information will be
written into Pcmod.err and the calculation will stop. The only information in the error file
is the type of constant missing and the atom types. Once the editor is started it can be
used to read the appropriate parameter file to add the missing constants.
8.13 Copy_To_Clipboard
Selecting this option copies the current structure window to the clipboard with all
color information intact. The clipboard can then be copied into a paint program for
editing, or it can be printed when a color printer is available.
8.14 Orient_XY Plane
Orient_XZ Plane
Orient_YZ Plane
These commands will orient the molecule in the selected plane. Select three atoms
using the Select command from the DrawTools menu, then select one of these options.
The first selected atom will be placed at the origin, the second atom will be placed along
the axis and the third atom will be rotated to lie in the plane specified. This option is
useful for orienting a structure before writing an input file for a molecular orbital
calculation.
8.15 Build Solvent Box/Solvate
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This option is used to build a box of solvent molecules or to solvate the current
molecule. If there is molecule in the structure window when this dialog is called the
dimensions of the smallest box enclosing
the current structure will be calculated
and displayed in the Mol Dimensions edit
boxes. The default solvent is set to water
but may be changed to chloroform,
octane or to the current structure. The
number of molecules desired must be
entered and the density may be changed
at this time. The cell size that is required
to contain the current structure and the
number of solvent molecules at the
entered density is computed and
displayed in the Cell Size edit boxes.
Hitting the OK button will causes the
solvent molecules to be added and the dialog box dismissed. If there is a current structure
on the screen it will be moved to the center of the box and the remainder of the molecules
will be added using the skew start method of Refson (K. Refson, Moldy v 2.9 …..). The
skew start method works well for small, compact molecules whose dimensions are nearly
spherical. If you want to build boxes of odd shaped molecules, those whose dimensions
are elongated in one dimension, then you should use the Build Periodic Box command
discussed below. Upon exiting this dialog the force field calculations are set to use
Periodic Boundary Conditions for minimizations and dynamics calculations. We
currently use a minimimum image convention, a spherical cutoff for dispersion
interactions and a particle mesh ewald method for long range electrostatic interactions.
Due to the organization of the code in PCMODEL these calculations are currently very
slow and PCMODEL is probably not the program of choice for production dynamics
calculations. However for short runs, initial testing and visualization PCMODEL works
fine.
8.16 Build Periodic Box
66
This menu options is useful for building periodic boxes of oddly shaped
molecules. There must be a molecule currently on the screen for this dialog to function.
The molecular dimensions of the current structure are computed and displayed in the Mol
Dimensions edit boxes. The number of molecules to include in the box and the desired
density must be input. Calc Cell Size computes the cubic cell required to hold the number
of molecules at the current density. Build Cell adds the appropriate number of molecules
to the cell using the “skew start” method (see above). The resulting cell can then be
visually examined for bad non-bonded interactions and a single point energy calculation
done to assess the extent of bad non-bonded interactions. If there are severe molecular
overlaps the added molecules can be erased using the Reset Cell button which returns the
cell to its initial state. The density can then be changed and the process of building the
cell can be repeated. By this interactive method a reasonable starting cell can be obtained
without severe non-bonded interactions. Energy minimization followed by dynamics runs
with increasing densities can be used to build a relaxed cell at the density desired for
study.
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68
Chapter 9 View Menu
Control Panel
Labels
Mono/Stereo
Stick Figure
Ball and Stick
Pluto
Tubular Bonds
CPK Surface
Dot Surface
Ribbon
RedGreen Stereo
Top View
Dipole Moment
Brings up a dialog box to scale, translate and rotate
structures in the structure window.
Brings up a dialog box to change the structure labels
Toggles between mono and stereo display
Display all structures as stick figures.
Display all structures as Shaded ball and stick figures.
Display all structures as Pluto type ball and stick figures.
Display all structures with tubular bonds.
Display all or selected structures with CPK surface.
Display all or selected structures with dot surface.
Display a Ribbon diagram of peptide or nucleic acid
backbone
Toggles red/green stereo display.
Turns on/off a top view of the current structure
Draws a dipole moment along with structure.
9.1 Control Panel
Selecting CONTROL_PANEL brings up a dialog box containing seven controls
which allow scaling, translation and rotation of the current molecular system.
The SCALE control allows the structure to be reduced or
enlarged. Enlarging the structure is useful when trying to select
atoms in congested systems, and reducing the structure can be
useful when visualizing large structures.
The three TRANSLATE controls move the molecular
system in the X, Y, or Z directions. The X direction is horizontal
on the screen, the Y direction is vertical, and the Z direction is
perpendicular to the screen.
The three ROTATE controls rotate the system around the
respective axes.
RESET_VIEW returns the molecular system to the
coordinates it had when the CONTROL_PANEL option was
selected. All translations and rotations are reset, but changes in
scale remain in effect.
RESET_SCALE resets the scale size to the default value. It has no effect on
rotations or translations.
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EXIT dismisses the dialog box.
To move one substructure relative to other substructures, use the MOVE
command under the SUBSTR menu.
9.2 Labels
Selecting LABELS brings up a dialog box through which the currently displayed
labels can be changed. The default is to only show bonds. Clicking on "OK" will close
this window, with the selected display type enabled, and this display type will be
remembered and made the default when you exit PCMODEL..
The options are:
Hydrogrens and lone pairs - places the letter "H" at each hydrogen position, and
displays lone pairs as a pair of dots. This does not add hydrogens or lone pairs, it only
displays them if they exist.
Bonds only (default) - removes all atom symbols from the display, but atoms and
bonds are shown in their normal colors. This is especially useful with large structures
which quickly become cluttered when atom symbols are displayed.
Atom numbers - labels each atom with its individual atom number. This is
useful for setting up files for GMMX, the global searching program, which works on
atom numbers. It is also useful when trying to interpret output given in terms of atom
numbers.
MMX Atom Types - labels each atom with its MMX atom type number. This is
useful for examining parameters used in the MMX calculations, since these are given by
atom type. (see Chapter 7 for a complete list of atom types and the corresponding
numbers).
MM3 Atom Types - labels each atom with its MM3 atom type number. This is
useful for examining parameters used in the MM3 calculations, since these are given by
atom type in the file MM3.PRM.
MMFF94 Atom Types - labels each atom with its MMFF94 atom type number.
This is useful for examining parameters used in the MMFF94 calculations, since these are
given by atom type in the file MMFF94.PRM.
AMBER Atom Types - labels each atom with its Amber atom type number. This
is useful for examining parameters used in the Amber calculations, since these are given
by atom type in the file AMBER.PRM.
Oplsaa Atom Types - labels each atom with its Oplsaa atom type number. This is
useful for examining parameters used in the Oplsaa calculations, since these are given by
atom type in the file OPLSAA.PRM.
Atomic Charge - labels each atom with its current atomic charge. This will be
zero (0.0) until a calculation is done, and the charges will be specific to the force field
used in the calculation.
70
Substructure number - labels each atom with a number representing its
substructure membership. This number is a value form 0 to 255 and is the sum of
2substructure number for all substructures for which the atom is a member.
Color by substructure - colors the bonds by the lowest substructure number at
each atom.
Color by Strain - During a calculation the energy for each interaction is
partitioned by atom. The individual atomic energy components are then normalized and
colors are assigned to each atom based on the magnitude of the energy with Red being
the most energetic, followed by rose, yellow, green, cyan, magenta, blue and gray.
9.3 Mono/Stereo
This option changes the default display between one structure (Mono) and two
structures displayed side by side in stereo. The stereo display can be rotated inward or
outward, though the use of STEREO option in the OPTIONS menu. In stereo mode the
two structures are rotated + and - three degrees from the mono structure to simulate a
stereographic display.
9.4 Stick Figure
Selecting this option returns the current drawing mode to the default stick figure
display of all atoms.
9.5 Ball and Stick
Selecting this option displays the current structure with small balls representing
the atoms and tubular bonds connecting the atoms.
9.6 Pluto
Selecting this option displays the current structure as a Pluto type ball and stick
figure with shading.
9.7 Tubes
Selecting this option displays the current structure with thick bonds.
9.8 CPK_Surface
This option displays the current molecular system as a CPK model
71
9.9 Dot_Surface
This option displays the current molecular system with a dot surface around it.
9.10 Ribbon
This option draws a ribbon for the backbone of a peptide or nucleic acid chain.
The display can be of the ribbon only, or the ribbon and a stick representation of the
structure itself. The type of molecule (acyclic protein, cyclic protein or DNA/RNA) must
be indicated.
The dialog box offers a choice of Oxygen-Oxygen (default) or swapped
orientation of the ribbon. Oxygen-oxygen produces smooth ribbons for alpha helices,
while swapped produces smooth ribbons for sheets.
The algorithm searches for the first N-terminus and draws the ribbon from there.
Once it cannot find another amide linkage in the chain, it stops there and draws the
ribbon. The ribbon display remains in effect until either the STICK_FIGURE option is
selected or the Ribbon dialog box is brought up and canceled. The ribbon display can be
rotated and translated, and can be printed.
9.11 Red/Green Stereo
Redraws the current structure in stick figure form using red and green images to
create a stereo image when viewed through red/green glasses.
9.12 Top View
Draws a second view of the current structure rotated by 90 degrees. The top view
is smaller and placed in the upper or lower corner, but this allows two views of the same
structure simultaneously.
9.13 Dipole Vector
Draws a vector representing the computed dipole moment of the current structure.
The dipole vector will be rotated with the current structure.
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73
Chapter 10 Compute and Force Field Menus
This menu contains the following options:
Minimize
Minimize the current structure(s).
Single Point
Calculate the energy of the current structure(s).
User External Charges Use charges read from external file, usually
Mopac/Ampac
Use Gasteiger Charges Assign charges based on Gasteiger’s sigma method
Normal Vibrational Modes Compute normal vibrational modes
Mopac
Run the semi-empirical quantum program Mopac
Ampac
Run the semi-empirical quantum program Ampac
Gaussian
Run the quantum chemistry program Gaussian
Gamess
Run the quantum chemistry program Gamess
PQS
Run the quantum chemistry program PQS (Linux
version only)
Orbitals
View the molecular orbital or electron densities
calculated in Mopac, Ampac, Gaussian, Jaguar, or
Gamess
Vibrations
View the normal vibrational modes calculated in
Mopac, Ampac, Gaussian, Jaguar, Gamess or
PCMODEL
GMMX
Run the stochastic conformational search.
Metropolis MC
Run the Monte Carlo conformational search.
Vibrational Mode Search Run search using low frequency vibrational modes
Dynam
Molecular Dynamics simulation.
Auto Dock
Simulated annealing search of lowest energy
interaction between two structures.
Manual Dock
Move the current substructure about the main structure
and compute the energy at each step
Batch
Read a multiple structure file and minimize all
structures or compute properties.
Rot_E
Rigid rotor evaluation of rotational energy barrier.
Dihedral Driver
Grid search with minimization evaluation of the
rotational energy barrier.
Relaxed Grid Search
Use Grid search as starting point then minimization
without fixing the dihedral angle.
Force Field Menu
MMX
MM3
MMFF94
AMBER
Oplsaa
Use the MMX force field.
Use the MM3 force field
Use the MMFF94 force field
Use the Amber 95 force field.
Use the Oplsaa force field.
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10.1 Minimize
This option optimizes the geometry of the current molecular system using the
currently selected force field. The current molecular structure is analyzed for atom types,
bonds, angles and dihedral angles and the appropriate constants are extracted from the
database of parameters. These parameters are found in the text files mmxconst.prm,
mm3.prm, mmff94.prm amber.prm or oplsaa.prm. The energy of the molecular system is
evaluated and written to the screen in the Output window, and then the minimizer is
called. The default action of the minimizer is to first do a first derivative minimization
until the gradient falls below 1, then a second derivative minimization until the gradient
falls below 0.0001. The minimizer attempts to lower the energy of the system by moving
the atoms. Every 5 iterations during the first derivative minimization, and then ever 2
iterations during the second derivative minimization the Structure window is updated
with the current geometry and the Output window is updated with the iteration number,
the atomic movement (in 10-5 Å units) and the energy (in kcal/mol). If the energy goes
up, or if the energy difference between two calculations falls within the convergence
criterion the calculation is stopped, the final energy and its components, the heat of
formation (for MMX and MM3 force fields) and the SE (strain energy) are written to the
Output window, and the Structure window is updated. In general, the energy minimum
found will be a local energy minimum. A calculation may be stopped at any time by
clicking the Stop Job dialog box.
The results, in abbreviated form, are written to the file pcmod.out. This file is a
record of all the minimizations done during the current session and can get quite large.
The default is to generate a minimum output, but this may be changed with the Printout
command in the Options Menu. Pcmod.out is overwritten every time you start
PCMODEL, so the file must be renamed to preserve a record of a particular set of
calculations.
A structure file, in PCM format, is automatically saved upon starting the
minimization and after every five iterations so that if the program crashes or is stopped
the last structure can be recovered. The filename is pcmod.bak and it is written in the
current directory. This file is overwritten every time a new minimization is begun, so to
preserve a structure it must explicitly saved with the Save command. The PCM file
format is the most concise way to save data since the energy data can be regenerated by
repeating the energy minization with the final optimized geometry.
A major problem in minimizing structures drawn without a template is that
hydrogens and lone pairs are often forced into inappropriate positions resulting in high
energy structures. It is a good idea to do an H-delete-H-add sequence (select H-A/D in
the TOOLS menu twice) then reminimize. For large structures, reminimize to be sure the
structure is fully converged. Since minimization is quite time-consuming with large
molecules, it is often economical to minimize the structure without added hydrogens to
get the three-dimensional structure approximately right prior to H-A/D and final
minimization.
In the MMX force field PCMODEL has access to a number of generalized force
field parameters ( i.e., torsional potentials dependent only on the two central atoms) to
which the program defaults if no standard MMX parameters are available. These
parameters are not optimal and energies produced with them should be considered
75
accordingly (however, geometries should not be too far off). The use of generalized
parameters is always noted in the output file PCMOD.OUT.
It is important to note that the MMX energy resulting from a minimization with a
pi calculation does not contain the potential energy of the pi system. So a comparison of
MMX energies for isomeric pi systems is invalid, just as a comparison of MMX energies
is invalid for structural isomers. A comparison of the heats of formation, on the other
hand, is appropriate. The only circumstance where MMX energies may be compared
directly is with conformers or diastereomers.
10.2 Single Point
SINGLE POINT does a single calculation of the energy of the current
structure(s). The calculation is begun just as for the MINIMIZE option, however the
calculation is stopped before the minimizer is called. The heat of formation is not
calculated during a single point calculation.
10.3 Use External Charges
This option forces PCMODEL to use any charges that were read into the program from an external
file. This option is often used with Mopac or Ampac files where the charge is computed and included in the
archive file. At this time charges are not read for Gaussian, Gamess, Hondo or Turbomol files.
10.4 Use Gasteiger Charges
This option forces PCMODEL to use charges computed by Gasteiger’s sigma model (Gasteiger
and Marsili, Tetrahedron, 36:3219-3288, 1980)
.
10.5 Normal Vibrational Modes
Since PCMODEL now has a full second derivative minimizer included the
normal vibrational modes of a molecule may be computed. You will first be prompted for
the name of a file to write the normal vibrational mode information, then a mass weighted
hessian matrix will be generated, diagonalized and the vibrational modes will be written
to the file. This file can be displayed using the Vibrate program (see below). MM3 does a
reasonable job with vibrational frequencies while MMX does not give reasonable
frequencies.
10.6 Mopac
This command attempts to execute the program Mopac using as input the current
structure. PCMODEL first attempts to find Mopac.exe in the current directory. If
Mopac.exe is not located in the current directory and PCMODEL does not have any
previous information about the location of Mopac.exe you will be prompted to provide a
path to the executable file. Use the browse dialog box to locate and select the program.
You should only need to do this the first time you run Mopac since the path information
will be saved when you exit PCMODEL. Your version of Mopac must be capable of
76
reading a filename from the command line since we will be passing the filename to
Mopac to execute. Serena Software markets a version of Mopac that does this. If you
have obtained a copy of Mopac from other sources or you have generated it yourself you
should check that this version can read the command line. After Mopac.exe is located,
you will first be prompted for a name for a Mopac input file that will be generated, and
then a dialog box for creating a Mopac format file will be presented. Either select from
the standard options or enter the keywords you wish to use on the Keyword line.
Mopac.exe will then be called with the filename a DOS type command window will be
displayed and the calculations will be run. When the calculation is complete the DOS
window will disappear and a new prompt will be displayed asking if you want to read the
geometric output of the Mopac calculation. If you chose Yes, then a file dialog box will
be presented for reading a Mopac Archive file. The filename will be “filename.arc”, that
is the name you first created with the three letter extension ARC appended. Selecting this
file will read in the new structure. If this file does not exist then the Mopac calculation
failed and you should look at the file filename.out (or FOR006) to discover the source of
the problem.
10.7 Ampac
This command attempts to execute the program Ampac using as input the current
structure. See the description given above for Mopac for instructions on running Ampac.
10.8 Gaussian
PCMODEL can directly run Gaussian 03 (or Gaussian 98). In the Windows
version the executable program to be run is g03.exe (not g03w.exe !!!!!).The Linux
version is still setup to run G98 and not G03 (please contact us if this is a problem). In all
versions a path to the Gaussian programs should be set before running Gaussian. (See the
Windows documentation for setting the Path. In Linux read the Gaussian documentation
for setting up the Gaussian environment variables) See the description for running Mopac
for more details on finding the Gaussian executable and generating filenames. The dialog
box for generating a Gaussian job file provides most of the standard options (see File
Menu save section for more information about the dialog box), however additional
options can be added by typing them on the keywords line.
10.9 Gamess
PCMODEL can directly run Gamess. See the description for running Mopac for
more details on finding the Gamess executable and generating filenames. The dialog box
for generating a Gamess job file provides most of the standard options (see File Menu
save section for more information about the dialog box), however additional options can
be added by typing them on the keywords line. The Windows version of Gamess has a
non-standard interface and while a job can be started from within Pcmodel we have not
found a way to save the output (PC_Gamess sends the output to the screen by default).
This is not a problem for the Macintosh or Linux versions of Gamess.
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10.10 Orbitals
This command executes the program Orbdraw which will display the molecular
orbitals and electron densities that can be computed by the quantum chemistry programs
Ampac, Mopac, Gaussian, Gamess and Jaguar. After the data file is selected the file is
read and the number of atoms, orbitals and electrons are displayed in a dialog box. Next
the orbital or density to display is selected from the View menu. The structure and
selected orbital or density will be drawn. The entire image may be rotated by dragging
the mouse with the left button depressed. The initial resolution for the display is
25x25x25 which gives a very crude picture but can be generated rapidly. A more detailed
picture can be generated by increasing the resolution and threshold value.
10.11 Vibrations
This command executes the program Vibrate which will display the normal
vibrational modes that can be computed by the quantum chemistry programs Ampac,
Mopac, Gaussian, Jaguar and PCMODEL. After the data file is selected and read a dialog
box giving the number of atoms and vibrations of the structure will be presented then a
stick figure of the vibrational spectrum will be displayed. A particular vibration can be
displayed by either pointing to the line in the spectrum and clicking the mouse, or be
selecting the vibration from the list of vibrations in the menu. Up to four vibrations may
be displayed at once and the structures can be rotated.
10.12 GMMX
This command initiates a conformational search on the current structure and up to
four rings and fifty rotatable bonds can be searched at one time. There are many options
available to control the search and they are discussed in the chapter on conformational
searching.
10.13 Metropolis-MC
This command initiates a Monte Carlo conformational search in internal
coordinates. All bond lengths, angles and dihedrals are included in the search.
10.14 Vibrational Mode Search
This command runs a conformational search that uses the low frequency
vibrational modes as search directions based on the method of Kolossvary and Guida
(Kolossvary and Guida, Journal of the American Chemical Society, 118:5011-5019).
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10.15 Dynam
DYNAM performs a molecular dynamics simulation using the leapfrog Verlet
algorithm. Selecting this option
brings up a Setup dialog box,
through which several
parameters of the simulation
may be set. The time step for
numerical integration (default 1
femtosecond) should never be
larger than 5 fs (and the
program may hang with this
value). The next options are
the initial temperature in K of
the sample molecule and the
surrounding bath (default for
each is 300 K). The next
option is the viscosity of the
medium in cp (default of 0). The next parameter is the time constant for heat transfer
(default value is 1, which results in transfer of energy from the bath to the sample). The
final parameter is the equilibration time before the run is sampled. You may sample the
run by clicking the Sample check box. The default sample time is 10fs. You will be
asked to provide a file name for the run. At each sample point a structure will be written
to the selected file. The run may be played back using the Movie option under the View
menu option.
Newton's equations of motion are used to calculate the position and velocity of all
the atoms at each time step. This method can be used to add or remove kinetic energy
from a molecule and to distribute the energy among various vibrational motions.
Processes that occur on the pico- and femtosecond time scale can be studied. The initial
structure should be minimized before starting the dynamics run. Initially the structure
will be drawn overlaid on the screen along with the kinetic and potential energy at the
current time.
The screen is updated at each timestep. Remember that vibrations occur on the
picosecond time scale and rotation about a bond, as in butane, may not be observed by
this method. Dynamics has application to large structures where strain can be relieved by
reducing van der Waals interactions.
10.16 Auto Dock
The AUTO DOCK option takes two or more minimized structures and attempts to
find the best interaction geometry. This is done using a simulated annealing algorithm.
The basic series of steps is:
1.
2.
3.
Evaluate the energy of the initial structures.
Randomly translate and rotate the second structure about the first.
Evaluate the energy of the new system.
79
4.
If the energy is lower than that of the original system, accept the new
structure and go to step 4.
If the energy is higher than that of the original system, use the Metropolis
algorithm to decide whether to accept the new structure. If the new
structure passes then go to step 4, otherwise go back to the previous
structure and then proceed to step 4.
Increment the counter. When enough structures have been analyzed,
lower the temperature which is used in the Metropolis algorithm. The net
effect of this scheme is to accept fewer uphill energy steps, and drive the
system to lower energies.
Selecting the DOCK option brings up a dialog box to set the initial conditions of
the calculation. The parameters are:
XYZ displacement (default 1 Angstrom)
Base angle
(default 15 degrees)
Start Temperature
(default 3 kcal)
Cooling decrement (default 0.1 kcal)
Energy Change/Cycle (default 0.2 kcal)
Stop on No Change (default 5 cycles)
The xyz displacement is the distance the
substructure will be moved in x, y or z times a
random number. The base angle is the rotation
angle to be used for rotating the substructure in x,
y or z times a random number. The starting temperature is given in Kcal as are the
cooling decrement and energy change per cycle. Clicking on OK brings up a dialog box
into which the filename for saving the results should be written, then starts the
calculation. When docking, the calculation may be aborted by hitting the ESC key on the
keyboard.
Since the simulated annealing procedure is stochastic, there can be no guarantee
of success or even that two successive calculations will end up with the same structure.
However, this method is superior to both manual and grid methods for docking studies.
Trial and error is required, and starting from several different conformations can be
useful. The structures to be docked should be located close together, since motion is
limited to the sum of the diameter of the main structure, plus twice the diameter of the
substructure plus 4 Å, even at the highest temperature.
10.17 Manual Dock
The Manual Dock options allows the user to take two minimized structures and
manuall move them about and evaluate the energy at each step. The entire ensemble can
be rotated by dragging the mouse, and the individual molecules with the control panel.
High energy interactions are shown in red as the structure is redrawn.
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10.18 Batch
The BATCH option allows the handling of multiple structure files without user
intervention. There are a number of options including both calculations and file
conversions. Selection of the BATCH option first brings up a file dialog box to get the
name of a file containing multiple structures (see FILE OPEN for a detailed description
of this dialog box). Any file format that supports multiple structures may be used. Next a
dialog box to select the desired options is presented. The current options include energy
minimization, computation of the surface area, volume or conversion of file type. One or
more of these options can be selected.
A FILE SAVE dialog is then presented to obtain the name and file type of the output file
for saving output structures. The input file is then read and the number of structures is
determined. A new dialog box is presented giving the number of structures, the default
starting structure, and the default filenames for the output and summary files. The output
file will be the name given in the FILE SAVE dialog and will contain the updated
geometries after minimization or file conversion. The summary file will contain a
summary of the minimization information including the MMX energy and the heat of
formation, surface areas or volumes depending upon the options selected. The various
fields of the dialog box may be edited to change the filenames and the default starting and
ending structure numbers. Clicking on OK starts the calculations, which will run
unattended until completion. The BATCH process can be stopped by selecting the STOP
JOB button. The cursor will change from an hourglass to a pointer when the calculation
is done. The bottom of the output window indicates the current structure number, and the
total number of structures to be calculated so that progress in the BATCH process can be
monitored.
10.19 Rot_E
The Rot_E option evaluates the energy required to rotate about a given bond,
using the rigid rotor approximation (meaning that the rotating ends are held rigid). The
current structure should be minimized and the two atoms of the bond of interest should be
SELECTed before ROT_E is selected. A dialog box appears, into which the step size
(default 10) and total rotation (400) are entered. Clicking on OK starts the calculation.
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The energy of the current structure is evaluated, then the specified bond is rotated by one
step size increment and the energy is re-evaluated. This procedure is repeated until the
total rotation value is reached, at which time a plot of energy vs. rotational angle is
displayed. This plot may be printed via its FILE menu. the ROT_E method is only
approximate since the energy is not minimized at each step of the calculation. This
method is useful for a fast scan of the rotational energy minima, which can then be
studied in more detail using the ROTATE_BOND and MINIMIZE options. A more
accurate barrier may be obtained by using the ROTATE_BOND command under the
EDIT menu to rotate the bond to a maximum value, then repeating the ROT_E
calculation.
10.20 Dihedral Driver
The DIHEDRAL_DRIVER option is an accurate, but more time consuming
alternative to the ROT_E option. With the DIHEDRAL_DRIVER option, a particular
dihedral angle is fixed at a specified value, and all the other degrees of freedom are
allowed to relax. Up to two dihedral angles can be driven in one calculation. Before
DIHEDRAL_DRIVER is chosen, the SELECT option from the TOOLS menu should be
used to mark the 4 atoms of the bond of interest. When DIHEDRAL_DRIVER is chosen
a dialog box will appear, displaying the selected atom numbers, along with the current
value of the angle. Values for the starting angle, final angle and step size for the first
angle must be entered. If two angles are to be driven, select "Get Second Angle". The
dialog box will be dismissed, and the four atoms forming the second angle can be
SELECTED. (The four atoms forming the first atom will be labeled with "d1".)
Selecting DIHEDRAL_DRIVER again will cause the dialog box to reappear, with the
data for the first and second angles present. The starting angle, final angle and step size
for the second angle must be entered. When all the required information has been
entered, click on CALCULATE. A new dialog box will appear for entering the filename
for the output structures. During the calculation, the coordinates of each step, along with
angle 1, angle 2 and the energy will be saved in a multiple structure file in either PCM or
MMX format for later display and analysis. The one or two dihedral angles are rotated to
their initial values and the energy of the structure is minimized, while holding the one or
two angles fixed. When the energy of that structure is minimized, the second angle is
incremented by its step size and the minimization is repeated. This procedure is repeated
until the final angle of angle 2 is reached, then angle 2 is reset, angle 1 is stepped to a
new angle and angle 2 is stepped through again.
82
dihedral driver dialog box. Choosing "last structure" (default) uses the previously
minimized structure for the next calculation, while choosing "original structure" reads the
original structure in, rotates the dihedrals to the specified angles, then calculates. The
"last structure" option is faster if machine I/O is slow, but can have problems with very
hindered structures where attached groups have a difficult time rotating past each other.
The result of all these calculations is an n by m grid of points where n is total
rotation of angle 1 divided by step size for angle 1, and m is the total rotation of angle 2
divided by step size of angle 2. The current limit on the grid size is 50 x 50.
The DIHEDRAL_DRIVER method is more accurate than the ROT_E option
since all other degrees of freedom are allow relaxed. However, it is more time
consuming, and in molecules with more than three rotatable bonds one needs to ensure
that other rotatable bonds have not rotated into a new energy minimum during the
dihedral driver sequence. This often happens when attempting to generate
Ramachandran plots of dipeptides.
Again, the calculation may be aborted by pressing the ESC key. To reset the
dihedral angle, use the RESET command under the MARK menu.
10.21 Relaxed Grid Search
Some of the problems with dihedral driver calculations include the combinatorial
explosion problem as more rotatable bonds are added and the failure to go to a minimum
energy because of fixed dihedral angles. While the first problem can not be solved the
second problem can with a relaxed grid search. The relaxed grid search uses the grid
points as the starting points for an unrestrained minimization. Selection of Relaxed Grid
Search first brings up a dialog box for entering the rotatable bonds of interest. The user
can select the bonds or select all the rotatable bonds. Selection of OK starts the
calculation. Initially all the rotatable bonds are set to 180 degrees and the energy is
evaluated. The bonds are the step sequentially through 360 degree rotations and the
structures are minimized. The program keeps track of the lowest energy found, removes
duplicate structures and sorts the structures by energy at the end. The Relaxed Grid
Search can handle many more bonds than the Dihedral Driver, but please remember that
the combinatorial problem still exists and if you choose to rotate many bonds you will
wait a long time for the results.
83
84
Chapter 11 Analyze Menu
Surface Area
Volume
Connolly
Calculate Surface area of molecule.
Calculate Volume of molecule.
Use the Connolly algorithms for calculating the Surface
area and Volume of a molecule.
Compare
Compare different structures.
Dihedral Map
Display the results of dihedral driver calculations.
Movie
Replay of all the structures in a multiple structure file
Dot Map
Generate a dot map from a multi conformation file
Multi Strucutre File Analyze a file containing multiple structures
Assign Sym
Assign point group symmetry.
11.1 Surface Area
This option calculates the exposed surface area of the current molecular system. A
stochastic algorithm is used which generates points on the surface randomly, determines
if the point is exposed or not, and counts the number of exposed and unexposed points. A
dialog box is used to set the number of points calculated for each atom (default 100), and
the number of times the calculation is repeated (default 20). Since the method is
stochastic the calculation is normally repeated several times and the average surface area
values are reported. The calculation may be aborted by pressing the ESC key.
When the calculation is complete, a window will appear with the total surface
area, saturated area, unsaturated area and polar area. (The atom types of the atoms are
used to divide the surface into non-polar, unsaturated non-polar and polar surface areas.)
11.2 Volume
This option calculates the volume of the current molecular system. Both
molecular volume (in cubic Å) and molar volume (in cubic cm) are reported. The
calculation may be aborted by pressing the ESC key.
11.3 Connolly Surface
This option calculates the surface area and volume of the current molecular
system analytically using the algorithms published by M. Connolly (M. L. Connolly,
"Analytical Molecular Surface Calculation", Journal of Applied Crystallography, 16,
548-558 (1983) and M. L. Connolly, "Computation of Molecular Volume", JACS, 107,
1118-1124 (1985
11.4 Compare
This option allows the comparison of two or more structures. The main structure
is, by definition, the structure with the lowest substructure number. If only one structure
85
is present when the Compare option is first selected, the structure is redrawn colored by
substructure and a dialog box is displayed so that a comparison structure can be read in.
If two or more substructures are present when COMPARE is selected, the structures are
redisplayed colored by substructure and the compare dialog box is then displayed.
Comparisons can be done an all atoms (default), heavy atoms only, or selected
atoms only. In order to use the Selected atoms option, the atoms must be SELECTed
using the SELECT button from the TOOLS menu before the COMPARE option is
chosen. The atoms may be marked in any order, but the calculations will match the first
selected atom of one structure with the first selected atom in the second structure, and so
on. Alternatively, one atom in the first structure may be selected, followed by the atom
to be matched to it in the second structure.
The other option in this dialog box are:
Calculate - starts a least squares calculation which attempts to minimize the
differences in the positions of the atoms being compared. The results of the calculation
will be given in the Compare window. The table of results will include 3 columns - atom
in structure 1, corresponding atom in structure 2, and distance between them in
angstroms. At the bottom of the table are the average difference between the distances,
and then the root mean square difference in the distance. If the output is too large to fit in
the window, the window can be scrolled. The structures will be drawn in the Structure
window overlapped with red lines connecting the atoms that are being compared. If the
structures overlap well, the red lines may not be visible.
Reset - clears the comparison arrays and removes the red lines between
comparison atoms from the drawing. This button is essentially used only for cleaning up
the screen.
Next Structure - allows reading in another structure for comparison. If two or
more structures are currently present, all but the main comparison structure will be
hidden. a file dialog box will be presented for selecting the desired structure file, the
structure will be read in and displayed to the right of the current structure, colored in the
appropriate substructure color.
Hide - makes all the comparison structures invisible. This is useful to keep the
screen from becoming cluttered when many structures are being compared.
Show All - makes all comparison structures visible. This is useful to display
several structures that have been compared.
Cancel - dismisses the Compare dialog box. All comparison structures are
deleted, and the main structure is re-displayed. It is necessary to erase all the comparison
structures since they occupy the same coordinates as the main structure (if the
comparison has been successful), and would cause any subsequent molecular mechanics
to fail.
86
11.5 Dihedral Map
This option allows redisplay of the results of a prior dihedral driver calculation.
A dialog box is presented prompting for the filename of the saved calculation. The file is
then read and a one angle or two angle plot is presented. See the FILE OPEN command
for a detailed discussion of the use of the file dialog box, and the DIHEDRAL_DRIVER
option in the ANALYZE menu for a full discussion of dihedral driver calculations.
11.6 Movie
This option reads a multiple structure file and shows all the structures in
sequence. The file formats currently supported
include PCM, MMX, Gaussian output and
Cambridge Structural Database. PCM type multiple
structure files are often generated during a
dynamics run, or part of a GMMX search. Thus the
results of a dynamics run can be replayed using this
options. Another use of this option is to view the
results of a Gaussian reaction coordinate scan.
You will first be asked to select a file for play. The
options in this dialog box are:
Play – Plays the movie.
Step – Steps through the file one structure at a time.
Loop – Continuously plays the movie.
Stop – Stops the Play or Loop.
Exit - Exits the dialog box and returns to PCMODEL.
The total number of structures in the file (5 in the illustration) and the current structure
number (1) will be displayed. The track bar reports the progress of the movie but does
not respond to clicks of the mouse.
11.7 Dot Map
This option reads in a file from a
GMMX search, compares a selected set of
atoms and orients each structure to overly the
first structure, then plots the position of a
selected atom from each structure relative to
the original structure. The result is a new
structure containing the position of every place
where the selected ‘dot’ atom can visit in the
various conformations. See Midland, M.M.;
Plumet, J.; Okamura, W.H. “Effect of C20
Stereochemistry on the Conformational Profile
of the Side Chains of Vitamin D Analogs,”
Bioorganic and Med. Chem. Letters 1993, 3,
87
1799-1804. for an application in the vitamin-D field.
After selecting Dot Map, a file-read dialog box will appear. Usually you will
want to use the first structure for the comparison. Next enter the atom numbers for the
comparison overlay. This can be done by either typing in the numbers separated by a
space or comma, or by using the Sel-Atm option from the Draw Tools. If Sel-Atm is
used, click on Update to fill in the edit box. Next select the atom for the dot. This can be
done by entering an atom number or by reselecting Sel-Atm, clicking on the appropriate
atom and then on Update. The dots will look bigger on the screen then in the print out.
Do not add hydrogens to the resulting structure, particularly if the dot atom is an oxygen
or nitrogen. An example of a
dot map is shown below.
11.8 MultiStructure
Multi
structure/conformation files
can be analyzed. There are
three main options- View
Structures, Analyze Structures
and Compare and Extract
Structures.
View Structures. The View structures option provides a quick way to step
through a file and look at individual conformations. A scrolling list of all the structures in
the file is shown and the file is displayed when selected from the list. This is very similar
to a standard file open, but the scrolling dialog box is not dismissed and no questions are
asked.
Analyze Structures. This option
allows you to perform query operations (distance,
angles etc) as well as surface area, volume and box
size calculations on a multi structure file. Clicking
on the Query buttons will provide a dialog box for
editing the query list. Queries may be entered by
using the Query button from the DrawTools and then
hitting the Update Queries button. If the multi
structure file is from a GMMX search, then the
energy information will be read from the file and
used to calculate a Boltzmann distribution for the
queries. You will be asked to give the name of an
output summary file.
88
Compare and Extract
Structures. This option allows
you to compare all structures in a
file or in two files, To extract all
structures which match a query or
to extract a set of structure from a
file. For example you may want
to retrieve all structures from a
GMMX search which have two
atoms 5.1+/-0.3 A apart
11.9 Assign Symmetry
This option attempts to assign the point group of the current structure using the cartesian
coordinates.
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90
Chapter 12 Substr Menu
Read
Create
Move
Connect
Fuse
Erase
Show Dummy
Don't minimize
Read a structure file and label the structure as a substructure.
Label the selected structure as a substructure
Moves the selected substructure.
Connect two structures.
Fuse two rings.
Removes the selected substructure from existence.
Display any dummy atoms in current structures.
Marks the selected substructure so that it will not be
minimized in a molecular mechanics calculation.
Substructures are a method for naming and manipulating individual molecules.
By default any structure read into PCMODEL using the OPEN command, or any
structure drawn in the Structure window is initially assigned to substructure number zero.
Several molecules may be drawn in the Structure window, but they all belong to
substructure zero and all will be moved, erased or minimized together. In order to
manipulate the structures individually it is necessary to mark them as substructures. The
commands available in the Substructure Menu provide all the facilities necessary for
handling substructures.
12.1 Read
The READ command reads a structure file into PCMODEL, marks it with a
unique substructure number and displays it to the right of the current structure. The
current structure is not erased. A file open dialog box is used for obtaining the filename,
filetype and path (see the FILE OPEN command for a detailed description of this dialog
box). Up to thirty two substructures may be created at one time in PCMODEL.
12.2 Create
The CREATE command marks a structure present in the Structure window as a
substructure. Before choosing CREATE, at least one atom in the structure must have
been marked with the SELECT button from the TOOLS menu. When the CREATE
command is chosen, a dialog box appears requesting a name for the substructure. This
name is associated with the substructure and can be used with the MOVE, ERASE, HIDE
and DON'T MINIMIZE commands.
12.3 Move
The MOVE command allows one substructure to be translated and or rotated with
respect to all the other structures. There are several methods for selecting the substructure
91
to move. One method is to use the SELECT button on the TOOLS menu to mark an atom
in the substruture to be moved before chosing MOVE. Alternatively, if no atoms have
been selected when the MOVE command is chosen, a dialog box will be presented listing
all substructures by name, and the substructure to be moved can be chosen by selecting
its name from the list with either the left mouse button or the up/down arrow keys. After
a substructure has been selected, click on OK, and the Control Panel dialog box will
appear. The translate and rotate controls will now only work on the selected substructure.
Rotation will be about the center of the selected substructure.
To change the substructure being moved, simply select an atom in another
substructure. The Control Panel controls will now operate on that substructure. Complex
docking can be accomplished by translation and rotation of selected substructures. To
rotate the entire collection of molecules as a unit it is necessary to Exit the Control Panel
dialog box, and then chose the CONTROL_PANEL option from the VIEW menu.
12.4 Connect
The Connect command connects two structures. First, SELECT the two
hydrogens to be removed to make the new bond (using the SELECT button in the
TOOLS men). The hydrogens will be removed and a new bond will be drawn between
the two heavy atoms that the hydrogens were attached to. Please see Chapter 3, Tutorials,
for a step by step description of connecting two molecules.
12.5 Fuse
The Fuse command fuses two rings. First, SELECT the two atoms in the first ring
and then two atoms in the second ring. The two atoms in the second ring will be removed
and the rings will be fused. The two rings should be recognized as separate molecules. If
you are uncertain use the Labels option from the View Menu and select Color by
Substructure. If the two rings are not different colors then they are not recognized as
separate structures. To make the two rings into separate structures select one atom in one
ring and use the Substructure Create option described above.
12.6 Erase
The ERASE command allows a substructure to be erased (deleted from
existance). As with SUBST MOVE, any atom in the substructure to be deleted may be
SELECTed before chosing ERASE, or if none are selected a dialog box will list the
possible substructures. There is no prompt for confirmation. Once the structure is deleted
it can not be recovered.
12.7 Show Dummy
The SHOW DUMMY commands redraws the structure with all dummy atoms
(atom type 60 in MMX) shown with gray dots over the atom. Dummy atoms can be
placed in a structure using the Dummy Atom type from the periodic table. Dummy atoms
have the same properties as hydrogens and can thus be minimized, but they are not
92
removed by HAD. The main purpose of Dummy atoms is to serve as place holders for
points of connection while building polymers or other large structures. See the Tutorial
Chapter of the use of dummy atoms in building poly-stryene.
12.8 Don't Minimize
The DON'T MINIMIZE command marks a substructure so that it will be ignored
during an energy minimization. This is a useful procedure when studying interactions
between surfaces and molecules, in which the interactions between the surface and the
molecules are of interest, but minimizing the surface would not be practical. This allows
building surfaces that are only two or three atoms deep, and thus would not maintain their
geometry if minimized, reading the surfaces into PCMODEL and then studing the
interaction of these surfaces with various molecules. As with SUBST MOVE, any atom
in the substructure to be deleted may be SELECTed before chosing DON'T MINIMIZE,
or if none are selected a dialog box will list the possible substructures.
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94
Chapter 13 Mark Menu
This menu contains commands that
H Bonds
Pi Atoms
Metal Coord
TS_BondOrders
Fix Distance
Fix Angle
Fix Torsions
Reset
Hydrogen Bonds
Pi atoms.
Set electron count, charge and coordination of metal atoms.
Set the bond orders for transition state bonds.
Fix a distance between any two atoms-up to 10 pairs
Fix an angle. Up to 10;
Fix a dihedral angle
Reset any of the above and also substructure membership.
13.1 H_Bonds
The MMX force field contains an extra term to correct deficiencies (in the
original MM2 force field) in describing hydrogen bonds. This term is turned on or off
depending upon whether the hydrogen bonds are marked. The default is to automatically
mark hydrogen bonds and to turn on the extra term in the force field. If the hydrogen
bond marking is turned off using the Reset option (see below), then the H_Bond option is
used to turn on the hydrogen bond term again. Hydrogen bonds are shown in red between
a donor hydrogen and acceptor atom when the distance between the two is less than 2.10
angstroms.
13.2 Pi Atoms
The MM2 and MM3 force field only contains one atom type to describe alkenes
(atom type 2), which is used to describe all types of unsaturation. The default parameters
for atom type 2 are set to reproduce the geometry of an isolated double bond, such as
ethylene, and will not accurately represent the geometry or energy of a conjugated system
such as butadiene or benzene. The solution to this problem is to do a simple pi vescf
calculation on conjugated systems. This calculation gives the bond orders of all the bonds
in the conjugated system, and these bond orders are used to adjust the stretching and
torsional parameters for those atoms in the conjugated system. The pi atom marking is
used to tell PCMODEL which atoms belong to the conjugated system and that a pi
calculation should be done. Selecting the Pi atom marking will automatically mark all
conjugated atoms. Reset is used to unmark the atoms. When Pi atoms are marked and
minimize is selected PCMODEL will first do a pi calculation on the conjugated system,
the parameters will be adjusted and then 15 iterations of geometry optimization will be
done. A pi calculation is then done on the updated geometry, the parameters are again
adjusted, and a complete minimization is done. When the minimization is complete
another pi calculation is done, followed by another minimization. The minimization ends
when no change in the geometry is observed after a pi calculation.
95
13.3 Metal Coordination
The Metal Coord option is used for
coordinating lone pairs and pi systems to a metal
atom, setting the electron count and geometry of
a metal, and setting the charge on the metal. The
metal atom of interest and any coordinated atoms
must first be selected using the SELECT button
on the TOOLS menu. After selecting Metal
Coord a dialog box will be presented showing the
metal atom symbol, the current charge if any, and
a set of radiobuttons describing the electron
count and geometry.
The force field model was designed with
no charges on the metal atoms (default charge is 0). Setting a charge will turn on
electrostatic interactions with other atoms and should be treated with caution. The
electrostatic model within molecular mechanics is not well defined or well tested, but it is
known that formal charges do not work well. You should check your calculations against
known compounds as you make modifications.
If the Metal Coord option is not used, all metals are assumed to be coordinately
saturated, and there will be no attractive potential between the metal and the lone pair or
p-orbitals of ligands which were not explicitly bonded during the DRAW phase of the
input. Atoms coordinated to the metal will be shown with a dotted line between the atom
and the metal.
13.4 TS_Bond Orders
If transition state atom types are used, their bond orders must be set before a
minimization can be done. When the TS_BondOrders option is selected a dialog box
appears listing the transition state bonds found and the current bond orders (if any are
known). The bond orders should be entered in the appropriate edit boxes. This data will
be written to the structure file when the file is saved.
13.5 Fix_Distances
The Fix_Distances option is used to fix the distance between two atoms, and up
to ten pairs can be fixed at one time. The two atoms whose distance is to be fixed should
be selected using the SELECT button on the TOOLS menu, then Fix_Distances can be
selected from the MARK menu. A dialog box will appear listing the two atoms, the
current distance and two edit boxes, one for the distance to fix at, and the other for a force
constant (default 5.0 mdyne/angstrom ). The distance is fixed by creating a bond
between the two atoms with the default distance set at the fixed distance, and with a force
constant input. The default force constant works for most cases. Fixed distances can be
combined with energy minimization or dynamics to build large structures with specific
interactions, for example, folded peptides (where the fixed distances come from NMR
experiments).
96
13.6 Fix Angle
The Fix Angle option is used to fix the angle made by three atoms and up to ten
angles can be fixed at one time. The three atoms of the angle should be selected first
using the Select button, and then Fix Angle from the Mark menu. A dialog box will
appear giving the atom numbers of the atoms of the angle, the current angle and edit
boxes for the angle to fix at and the force constant to use.
13.7 Fix_Torsions
The Fix_Torsions options is used to fix up to two dihedral angles. The four atoms
defining the dihedral angle must first be selected using the SELECT button in the
TOOLS menu. The Fix_Torsion option will then present a dialog box listing the four
atoms, the current angle, and an edit box for entering the angle to fix at. The routines
used for fixing a torsion are the same as those used for the dihedral driver and are limited
to two dihedral angles at one time.
13.8 Reset
The Reset option brings up a dialog box which allows resetting all the options
given above, and also substructure membership.
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98
Chapter 14 Options Menu
This menu contains commands that
Printout
Dielc
DPDP
Minimizer
MMX_PI Options
Added Constants
Standard Constants
Stereo
Pluto
VDW Surface
Dot Surface
Sets the amount of output in the file PCMOD.OUT.
Resets the dielectric constant.
Switch between dipole/dipole and electrostatic calc.
Control which minimizer to user.
Set options for Pi calculations.
Allows the addition of user defined constants
Forces the use of the default data set
Changes the direction of rotation of stereo display.
Set Pluto options
Set VDW display options
Set Dot Surface display options.
14.1 Printout
The PRINTOUT option sets the level of information written to PCMOD.OUT.
The default is to write a minimal output file which lists that atomic charges, any
generalized constants used and the initial and final energies for a calculation. Full
printout gives a complete list of all interactions used in the calculation of the final energy.
Each bend, stretch, torsion, VDW interaction and charge-charge interaction is listed with
constants used, current geometry and the energy contribution from that item. A full
printout can be quite long. The current option (Full or Min-imal) is indicated in the
Output window.
14.2 Dielc
The DIELC option sets the dielectric constant which has a default of 1.5. It is rare
for increases in DIELC to reproduce the properties of molecules in higher dielectric
solvents, so this should be used with great care. If a negative value for DIELC is input,
then the charge-charge interaction will be calculated with a distance-dependent dielectric
constant (Dielc = f(Rij )), an option that is used successfully in the AMBER program
when attempting to model the effect of a polar solvent or lack of counterions. Setting
Dielc to -1. will adversely effect calculations done with dipole-dipole interactions.
14.3 DPDP
The DPDP option allows choice of either dipole-dipole or electrostatic
calculations. The default in PCMODEL is to use electrostatic calculations with the
charges being calculated from the default bond moments. This is a more general
procedure and allows incorporation of charged species. However, the MM2 force field
99
was originally developed with the dipole dipole method. The charges for the electrostatic
calculations are, in most cases, derived from the bond dipoles programmed into MM2 for
the bond dipole option, although heteroatom pi systems will also contribute charges. The
default electrostatic calculations use the MM2 charges but also include the dielectric
constant in the denominator of the energy expression. Electrostatic calculations should be
used with atoms having charges (e.g., N+, C-) and they will also allow the halogens to be
considered as ions if they are not directly bonded to any other atom. The only reason to
use DP-DP is to compare a calculation to an MM2-like calculation.
14.4 Minimizer
This options controls the default actions of the minimizer. PCMODEL now
includes a first derivative minimization method, BFGS, and both truncated NewtonRaphson and full Newton-Raphson second derivative minimization methods. The default
behaviour is to do a first derivative minimization until the gradient falls below 1, and then
a second derivative minimization until the gradient falls below 0.0001. This dialog box
allows you to switch to a first derivative only minimization, second derivative only
method or to the mixed method. While the mixed method appears to be the most robust
method for general use, there are times when the path taken through conformational
space is dependent upon the choice of minimizer.
14.5 MMX_PI Calculation Options
This option allows setting a number of options for the pi calculation. The choices
are:
RHF or UHF
Choose between Restricted
Hartree Fock and
Unrestricted HF
calculation. For closed
shell molecules with all the
electrons paired the RHF
option should be used. The
UHF option is used for
species with unpaired
electrons (monoradicals,
diradicals etc.) or for
higher spin states.
Mult Set the multiplicity of the system. The default is 1 for a singlet state.
Huckel or Full SCF Set the type of the initial pi calculation. The default is to do
a simple Huckel calculation which ignores the geometry of the pi system in determining
the bond orders. This method is preferred when the starting geometry is poor. The Full
SCF uses the geometry of the pi system in determining the bond orders and will give
better bond orders if the starting geometry is close to the final geometry.
100
Non-Planar or Planar Pi System- This tells PCMODEL whether the entire pi
system is planar or non-planar. The default is to assume a non-planar pi system and check
for non-planarity. Use the Planar option only if the entire pi system is co-planar.
All of these options are reset when a structure is erased.
14.6 Added Constants
The Added CONSTANTS option forces allows the use of a file of user defined
constants to be used in addition to or as replacements for the standard constants. The user
is prompted for the name of the added constants file, which must use the same format as
the standard constants file. PCMODEL checks as the added constants are read and
replaces the standard constants if one exists or adds the new constant to the bottom of the
parameter list if no previous constant has been defined. To return to the standard
constants use the Standard Constants button below.
14.7 Standard Constants
The STANDARD CONSTANTS option forces PCMODEL to use the default
constants. All parameter arrays are set to zero and the default parameter files,
mmxconst.prm is read
14.8 Stereo
The Stereo option sets the direction of rotation for the stereo display. The options
are to rotate the two structures inward (cross eyed display) or outward (wall eyed display,
default). The selecteds option remains in effect until changed.
14.9 Pluto
Choosing this option brings up the following dialog box:
Ang1 and Ang2 - Control the
position of the light source.
Shade – Controls the density of the
shade lines, lower number gives more lines.
Ball_Stick or CPK – Produces a
ball and stick structure or a space-filling
structure.
Bond Taper – A higher number will
give a greater perspective taper to bonds.
Bond Radius – Controls how wide
the bonds are when drawn. A large number
gives wider bonds.
Bond Lines – How many lines are
101
drawn per bond.
The default values are given in the example dialog box.
14.10 Vdw Surface
Upon choosing this option the following dialog box appears:
The atoms to be displayed in
this manner can be all atoms, heavy
atoms only or selected atoms only. In
order to use the Selected-atoms option,
the atoms must be SELECTed using
the SELECT button from the TOOLS
menu before the CPK option is chosen.
The radius for the CPK model can be
varied from the van der Waals radius
(1.0, default) down to 0.65 (the .20 ball
and stick option has been removed). The “color by” option has not been implemented.
The CPK model continues as the default display until either the STICK FIGURE option
is chosen, or the CPK_Surface dialog box is brought up and canceled. The CPK models
can be rotated and translated. CPK models, dot surfaces and Ribbon diagrams can all be
displayed at the same time.
14.11 Dot Surface
Choosing this option brings up the following dialog box:
The dot surface is generated using the Lee and Richards algorithm and two
different radii are available - the van der waals radius (default) or a water surface (van der
waals + 1.4 Å). The CHARGE option uses the van der waals radius and colors the
surface by charge, with redder colors representing positive charge and bluer colors
representing more negative charges. White is used for neutral atoms.
102
The atoms to be displayed in this manner can be all atoms or selected atoms only.
In order to use the Selected atoms option, the atoms must be SELECTed using the
SELECT button from the TOOLS menu before the DOT_SURFACE option is chosen.
The Dot Spacing option controls the number of dots displayed on the surface. A
closer spacing gives more dots, but takes longer to draw and manipulate (rotate and
translate).
The dot surface model continues as the default display until either the
STICK_FIGURE option is selected, or the DOT_SURFACE dialog box is brought up
and canceled. CPK models, dot surfaces and Ribbon diagrams can all be displayed at the
same time.
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104
15 The MMX Force Field
15.1 The MMX Force Field
The MMX force field embodies many years of work by J.J. Gajewski and K.E.
Gilbert to extend and improve upon the MM2 force field of N. L. Allinger. The starting
point for MMX was the MM2(77) program of Allinger. To this was added the VESCF pi
routines from MMPI, and the concept of generalized parameters from C. Still. The goal
of this work was to be able to treat more compounds of interest to synthetic and
mechanistic organic chemists. For example, such functional groups as radical, cations and
anions are not handled in MM2. The current version of MMX recognizes nearly 60
different atom types including radicals, anions, cations, transition metals and transition
state atoms. The table below lists the atom types, symbols and a brief description.
ATOM TYPE NUMBERS - MM2/MMX
Type
Symbol
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
C
C
C
C
H
O
O
N
N
N
F
Cl
Br
I
S
S+
S
S
Si
LP
H
C
H
H
P
Description
Carbon, SP3
Carbon, SP2 (Alkene)
Carbon, SP2 (Carbonyl)
Carbon, SP
Hydrogen (note special types 21,23,24,28 below)
Oxygen (singly bonded)
Oxygen (doubly bonded)
Nitrogen, SP3
Nitrogen, SP2 of enamines and amides
Nitrogen, SP
Fluorine
Chlorine
Bromine
Iodine
Sulfide (-S-)
Sulfonium (>S-+), NOT sulfoxide!
Sulfoxide-use double bond to O.
Sulfone-use double bonds to O.
Silane
Lone pair (:)
Hydrogen, Hydroxyl (-OH)
Carbon, Cyclopropane
Hydrogen, Amine (NH)
Hydrogen, Carboxylic acid (COOH)
Phosphorus [PRELIMINARY]
105
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
B
B
H
C.
C+
Ge
Sn
Pb
Se
Te
D
N
S
Se
Ar
Boron (trigonal)
Boron (tetrahedral)
Hydrogen (enol)
C Radical
Carbonium ion
Germanium
Tin
Lead
Selenium
Tellurium
Deuterium
Nitrogen SP2 of Imine
Thion sulfur
Selenoxide Se
Aromatic Carbon (1.40Å bonds between 40-40)
(Use this atom type only when conjugation effects are not a
concern. If conjugation effects are important, use
and mark it as a pi atom.)
N+ Ammonium nitrogen
O- Oxy anion
TS Boron
Not Used
TS Hydrogen
Onium ion, also metal bound carbon monoxide
Pentavalent phosphorous
Carbanion
Transition State (TS) Carbon
Transition State (TS) Carbon
TS Trigonal carbon bonds to C*
TS Pentavalent carbon bonds C*, O#, and I%
TS Oxygen bonds to C# and C%
TS Iodine bonds to C% in SN2
TS Nitrogen bonds to C#
Cyclobutane carbon as in MM3
Cyclobutene carbon as in MM3
WILD CARD 2
WILD CARD 3
Spherical water
normal carbon
41
N+
42
O43
B#
44
xx
45
H*
46
O+
47
P5
48
C49
C*
50
C#
51
C$
52
C%
53
O#
54
I%
55
N#
56
C
57
C
58
Z1
59
Z2
60
Aq
???? other types
Parameters were developed by standard methods, using literature values,
interpolated values from known parameters, or chemical intuition, followed by
comparison to experimental data for geometries and heats of formation. The complete
parameter set is found in the data file mmxconst.prm..
106
15.2 Minimization with PCMODEL (hints)
Whenever a molecule is minimized in PCMODEL, an Output window displays
the results of the calculation. The upper portion of the Output window displays the total
energy, as well as a breakdown by component, dipole moment, heat of formation (Hf)
and Strain Energy (SE). The components of the energy are Str (stretching), Bnd
(bending), StrBnd (stretch-bend cross term), Tor (torsion), VdW (Van der Waal
interactions), and QQ (charge-charge electrostatic interaction).
The lower portion of the Ouptut window indicates the dielectric constant that was
used in the calculation, whether default or added constants were used, and the current
level of printer output (default is minimal).
The MMX energy has a correction for 1-3 electrostatic interactions when two
non-zero charge atoms are attached to a sp3 carbon. This correction is not made with any
other central atom and can be a source of error. If there are no cations or anions in the
structure or no charged pi systems, a single point calculation using the DP-DP interaction
should give a better energy for polar molecules.
A major problem in minimizing structures draw without a template is that
hydrogens and lone pairs are often forced into inappropriate positions, resulting in high
energy structures. It is a good idea delete then re-add hydrogens (by pressing H/AD on
the TOOLS menu twice) then reminimize. Also, for large structures reminimizing is
recommended (select MINIMIZE again) to make sure the structure is fully converged.
Since minimization is quite time-consuming with large molecules, it is often
economical to minimize the structure without added hydrogens to get the threedimensional structure approximately right prior to adding hydrogens and doing a final
minimization.
PCMODEL has access to a number of generalized force field parameters
(torsional potentials dependent only on the two central atoms) to which the program
defaults if no standard MM2 parameters are available. These parameters are not optimal
and energies produced with them should be considered accordingly. However, the
geometries can be considered fairly accurate. The use of generalized parameters is always
noted in the output file PCMOD.OUT.
All of the parameters for ligands directly bonded to a metal or for ligands
coordinated to a metal assume no charge on the metal. A charge on the metal can be set
using the Metal_Coord choice in the Mark Menu. This option should be used only if the
electrostatic attraction between ligands and a metal are to be employed and not formal
bonding or coordination via the Metal_coord option. Formal charges are not a good
representation of charge distribution in metal complexes.
The heat of formation calculation will be marked as INC (incomplete) if some
bond parameters are missing. The pi contribution to the heat of formation depends on
whether the default point charges or the bond dipole interaction are used (NDC=0). The
default uses atom contributions and the pi energy calculated; if NDC=0, a bond
contribution scheme based on pi order is used. The list of bond types handled by the
former option is incomplete relative to the latter; however there is no warning that this is
the case. It is important to note that the MMX energy resulting form a minimization with
a pi calculation does not contain the potential energy of the pi system. So, a comparison
of MMX energies for isomeric pi systems is invalid, just as a comparison of MMX
energies is invalid for structural isomers. A comparison of the heats of formation, on the
107
other hand, is appropriate. The only circumstances where MMX energies may be
compared directly is with conformers or diastereomers.
15.3 Transition State Atoms
Transition states can be modeled using PCMODEL. The eleven transition state
bonds that are recognized are:
C* - C*
C# - C#
C - H*
C* - H*
C# - B#
C* - C$
C# - O#
C* - C%
C% - I%
C% - O#
C# - N#
e.g. forming bonds in Diels Alder rxn or in Cope rear.
e.g. forming bonds in Diels Alder or breaking bonds in Cope.
e.g. allylic C-H bond in ene reaction.
e.g. forming H-C bond in ene reaction or hydroboration.
e.g. forming B-C bond in hydroboration.
e.g. forming bond in addition of nitrile oxide sp C to sp2 C.
e.g. breaking bond in Claisen rearrangement.
e.g. carbon nucleophile in SN2.
e.g. leaving group bond in SN2.
e.g. oxygen nucleophile in SN2.
e.g. breaking bond in an Aza Cope rearrangement.
These transition state bonds are fractional. The user must input a bond order for each
when requested by PCMODEL. Note that Diels Alder transition states are "early" and
have both bond orders roughly 0.3 for symmetrical addends. Bond orders of 0.3 will
mimic the nitrile oxide addition to ethylene transition state calculated by Houk (make
sure that the nitrogen has a double bond so that it is a type 37 atom). Cope transition state
bond orders depend on substitution, as do all of these as revealed by secondary deuterium
isotope effect studies. That is why the user is in complete control of the transition state
bond orders.
For other pi atoms in pericyclic transition states use C.s, the radical carbons, eg.
for C2 and C5 of 1,5-hexadienes in the Cope transition state or for C2 and C3 of
butadiene in the Diels-Alder transition state. NOTE: You CANNOT do a Pi calculation
on C* or C#; Further, the bonds between the C.s in the transition state are fixed at 1.40 Å
and have k=7.0.
PCMODEL generates a set of transition state atom parameters from the fraction
bond input by the user. These parameters for C* and C# force 90 degree angles between
C*1 C*2 and any other atom as the fractional bond order approaches 0. This angle will
spread to 109 degrees as the fractional bond order approaches 1, as will C#-O#. The
parameters generated for B# additions attempt to mimic the acute angle between B# and
C#-C* with appropriate hydrogen angles and distances. The angle at C$ of a C$-C* starts
at 180 degrees for no bond and goes to 120 when the bond order approaches 1. The
angles of the bonds to C% start at 109 with C%-I% bond order of 1 and an incoming
nucleophile bond order of 0.; they go to 120 when both bond orders to C% are equal, and
then return to 109 as the incoming nucleophile -C% bond order approaches 1 and the
C%-I% bond order approaches 0.
108
The transition state bond natural bond lengths are determined by the input bond
orders according to Badger's Rule cast in Pauling bond order terms:
distance = distance of fully formed bond - 0.6•ln (bond order).
force constant = force constant for fully formed bond * bond order.
The constant 0.6 is twice as large as the Pauling constant for bond orders greater than 1.
This value is used because it reproduces the structure of the Diels-Alder transition state
calculated by Houk from 3-21G basis set, if the kinetic isotope effects determined at
Indiana on the Diels- Alder reaction are used as input bond orders.
15.4 Pi Calculations
The constants in PCMODEL will reproduce acids, esters, amides, eneamines,
vinyl ethers, carboxylates, nitro groups, alpha, beta unsaturated aldehydes and ketones,
allyl cations, anions, and radicals NOT conjugated with a pi system without having to do
a pi calculation on these specific functional groups. However, adjacent pi systems will
not "experience" the pi electron effect of these groups unless they are included in a pi
calculation. Any diene or material with more than four conjugated pi electron should be
subjected to a pi calculation (See hints on specific atoms below). If a pi calculation is
done with these atoms, non-delocalized constants are used and are adjusted by the bond
orders. Pi calculations must be done on other delocalized moieties such as alpha, beta
unsaturated imines, nitriles, etc. The pi calculation can be done as either a closed shell or
open shell type so that monoradicals are handled reasonably unlike earlier versions of the
MM2 force field such as is found in MMX87, MMPMI, MMP2, or MMP1. The pi
portion of the code, which is the R.D. Brown VESCF procedure, has been checked
against MMP1 (QCPE 318).
15.4.1 Pi Atoms
The pi atoms treated originally are:
C sp2
(type 2)
C
(carbonyl carbon type 3)
C sp
(type 4)
O sp3
(type 6)
O
(carbonyl oxygen type 7)
N
(amide-like type 9)
N
(nitrile type 10).
The additional new pi atoms are:
C.
C+
N+
O-
(type 29)
(type 30)
(ammo-& immonium type 41)
(type 42)
109
N
C-
(imine type 37)
(type 48).
MMP1 and MMP2 will not recognize any of these atoms. Pi calculations cannot be
performed on third row elements like S or P, nor can any of the halogens be included.
Compounds with twisted or pyramidalized monoolefins should be submitted to a pi
calculation for comparison purposes.
15.4.2 Heat of Formation of Pi Systems
The contribution of the pi system to the heat of formation depends on pi bond
orders. First the number of double bonds in a non-charge-separated valence bond
structure is determined from the number of filled MOs minus the appropriate number of
electrons from any type 6, 7, 9, 29, 42, and 48 atom. The number of each type of double
bond is multiplied by the contribution each makes to the heat of formation as described in
MM2, e.g. 22.8 for each C=C, -24.5 for each C=O, 31.0 for each C=N, etc. Bonds
involving a type 6, 9, 29, 30, 42, or 48 atom have a contribution of a constant which is
roughly that if the electron(s) were not delocalized, e.g. 0. for 03-09, -16.7 for 02-06 and
for 03-06, 12. for 02-48, etc.
In MMX for pi atom pairs of the latter description, the pi bond order multiplies a
negative constant unique to each so as to decrement the heat of formation; this seems
reasonable-higher bond order, lower energy. However, for pi atom pairs not in the latter
category, a pi bond order between 0.4 and 0.85 will decrement the heat of formation by a
constant characteristic of the atom pair; the decrement falls of as rho2 when rho is less
than 0.4 and as (1-rho)2 when rho is greater than 0.85. It is this function which allowed
the use of bond orders for the heat of formation calculation; however, it does poorly for
larger >C8 carbocyclic pi systems.
The calculation of the heat of formation of the pi system depends on whether only
type 2 (olefinic), type 29 (radical), type 30 (cation), and type 48 (carbanion) carbons are
present or (& heteroatoms without a charged atom or C.) or whether N+, O- or C.,C+, or
C- and heteroatoms are present. In the former cases with just trigonal carbon, the sum of
pi bonds multiplies 90.2 kcal/m (the strength of a strainless Csp2-Csp2 bond). To this is
added the compression energy using 1.51 as the strain free value ( the quadratic constant
is 517 kcal/ang*2). To this is added the Pople pi energy (a negative quantity); then the
contribution of each pi atom to the pi portion of the heat of formation is added (these
values are 92.8 kcal/m for a pi atom attached to one other pi atom; 141.95 for a pi atom
attached to two others; and 189.0 for a pi atom attached to three others).
A similar parameterization applies to other cases within the first category. In the
latter cases, each C=C contributes 11.2 kcal/m to the heat of form.; then the compression
energy is calculated using 400 kcal/m as the constant. Finally, the difference in the total
bond order of the pi system relative to that of the number of classical pi bonds is
multiplied by 35 kcal/mol to obtain the pi stabilization. The contribution from the other
bonds is similar to that in MMPMI where the bond orders key the contributions to the
heat of formation. Generally the heats of formation are good to 2 kcal/mol, but it is
unclear where large deviations might occur.
110
15.5 Transition Metals
Note that many basic atoms can be docked (not attached with a bond that appears
in the connected and attached atom lists) with their lone pair to a metal. Alternatively,
atoms can be attached with a bond replacing the lone pair, and despite the increase in
positive charge at the atom, the neutral atom types above should be used, e.g. M-N
tetravalent (use type 8 not type 41).
TYPES of BONDS to Metals that MMX will recognize (Use the Atom Types option in
the LABELS of the VIEW Menu to make sure that the proper atom types are used):
to NITROGEN/
M <- :N- type 8
\
amino, can dock for automatic Hs & lps or specify all four bonds
including Hs (no lp).
M - N< type 9
pair
amido, to coordinately saturated M, specify 0944 bond. no lone
M - N-C= type 9
pair
\
M <-:Nsp type 1
recognizes
amido, N next to unsaturated carbon, specify 0944 bond, no lone
on N.
nitrile or nitrogen coordinate or specify all bonds (no lp), MMX
this relative to nitride below.
M N: sp type 10
nitride
M = N+< type 41
amido, to coordinately unsaturated M, specify 4144 bond.
M <-:N= type 37
\
imino, coordination-requires docking; or specify all four bonds
including metal.
M -N:= type 37
bond,
imido, to coordinately saturated M, eg. bent nitrosyl, specify 3744
leave lone pair on N.
M = N+= type 41
4144
group.
M - N: sp type 10
imido, to coordinately unsaturated M, eg. linear nitrosyl, specify
bond, MMX will recognize the difference between this and amido
to OXYGENM - O - R type 6
two lone pairs on O, coordinately sat'd metal.
M = O:: type 7
oxo, two lone pairs on O.
111
M - O- type 42
M <-:O< type 6
ether and
pair.
M - O:=C type 7
two lone pairs on O-, coordinately sat'd metal.
coordination between 44 and lone pair on type 6, can dock with
alcohol oxygen; alternatively, specify three bonds and lone
one lone pair on O, MMX recognizes this and oxo
+ M = O- type 46 one lone pair on O+, coordinately unsat'd metal.
to HALOGENM - F, M - Cl, M - Br, M - I, can be terminal or bridging, specify each bond.
to HYDROGENM - H type 5
M - H* - M type 45
to CARBON/
M - C- type 1
\
terminal hydride.
bridging hydride.
sigma alkyl, specify 0144 bond.
M - C= type 2
sigma vinyl, specify 0244 bond.
M - C<| type 22
sigma cyclopropyl, specify 2244 bond.
M - C=O type 3
sigma acyl & bridging carbonyl, specify 0344 bond.
M - CO+ type 4
terminal carbonyl or terminal cyano, specify 0444 bond; Note that
terminal carbonyl has a triple bond between C & O so that the O is
PCMODEL will recognize this if a neutral O is used.
a
really O+
M - C+< type 30
metal carbene, specify 3044 bond.
M - C:< type 48
specify 4448 bond, possible bridging with lone pair.
/
M <-:C- type 48
\
coordination only.
112
to SULFURM -:S:- R type 15 two lone pairs on S, coordinately sat'd metal.
M = S:: type 38 two lone pairs on S.
M <-:S:< type 15 coordination between 44 and lone pair on type 15, can dock for
thioether
and thiol sulfur or specify three bonds to S- one lone pair.
M = S:+- type 16
one lone pair on S+, coordinately unsaturatedd metal.
to PHOSPHOROUS/
M <-:P- type 25
\
coordination to lone pair or specify all four bonds (no lp).
to METALSM - M 4444 bond MMX will alter natural bond distances if bond order is specified.
COORDINATION is possible with the following ligands:
::O< type 6
::O= type 7
/
:N- type 8
\
:N type 10
::S< type 15
/
:P- type 25
\
/
:C- type 48.
\
Pi coordination also from types 2, 4, 29, 30, 40, and 48 carbons.
113
Chapter 16 File Formats
16.1 PCM File Format
The PCM file format is a free format, context driven grammar for the description
of molecular structures. This gives the user more and easier control of their structure
files for additions and corrections, and leaves room for expansion of the definition of the
force field. The context also allows for greater error correction within the program.
At the end of this section is an example of a PCM file which describes the
structure in Figure 6.1. Key words have been printed in bold for clarity. In this structure,
we have included substructures, Pi atoms, hydrogen bonding, a metal, atomic charge, and
coordinate bonds. The features of the file are fairly straight forward. From the top is the
file type marker {PCM which indicates that the file is a PCM type file. This is required
of all PCM files so that PCMODEL and MMX will recognize them. Immediately
following the file type marker, on the same line, is the name of the structure. This name
may be up to 58 characters long.
On the next line appears NA followed by a number. This tells the number of
atoms in the structure. This number is optional and is used only to check for consistency.
Next, is SS 1 which introduces substructure number 1 and gives it a name which
follows. The name can be up to 20 characters long. This is also optional. Currently, this
statement only gives the substructure a name though at some point, it may be used to tell
other aspects of the substructure.
The fourth line contains FLags: EINT UV. Currently, the following flags are
defined:
EINT 0:
dipole interaction energy will be calculated excluding interactions
between dipoles with a common carbon.
1:
as above but with all interactions.
2:
dipole interaction calculation suppressed.
3:
charge interaction energy will be calculated (excluding interactions
between atoms bound to a common atom). If this option is used
you must
read in atomic charges.
4:
charge interaction energy used. Charges calculated from bond
dipoles
with additions for pi atom charges.
UV
0:
if pi calculation, will be prompted before minimization:
Number of electrons?
Singlet, doublet, triplet, ?
RHF or UHF calculation ?
if singlet, RHF then restrictions on wave function?
# of identical pairs of atoms?
atom numbers of pairs?
# of sets of identical bonds?
atom numbers of bonds of bond pairs ?
1: default to singlet RHF pi calculation - no questions.
114
2: default doublet UHF pi calculation (for mono radicals) no questions.
DIELC
values give a
dipole-dipole
Floating point value of the new dielectric constant. Negative
distance dependent dielectric constant. (nonsense with
interactions).
Line 5 contains the first atom record. After the atom specifier AT, the index
number appears. These are the atom number and are used to reference the bond numbers.
Next after some separator, usually a comma though a colon or a space will do, is that
atom type number (see chapter 7 for a description of atom types). In the case of metals,
the metal symbol is included in this space instead of the atom type number as in the sixth
atom record.
Next, appears some separator; we use a colon here for clarity. Then in order, is X,
Y, and Z in angstroms. After the next separator, the bond marker, B, appears the list of
bonds attached to the atom. 2,1 means a bond to atom two is a single bond. In atom 6,
you will notice 10,9, which indicates a metal coordinate bond (type 9) to atom 10.
At the end of the first few lines is a C followed by a number. C specifies a
charge. Again looking at atom 6, an M appears. Following M is the specified electronic
state of the metal, in this case 3 for low spin. R introduces the covalent radius. This
number is used to determine the bond lengths of all ligand attachments to that metal.
The record for atom 8 contains an H which indicates that it is a hydrogen bonding
hydrogen. Atom 9 contains a P which marks it as a pi atom and an S, which refers to the
list of substructures of which this atom is a member. The comma after the S is optional
but is added for clarity.
Finally, the structure file is closed with a }. This is mandatory so PCMODEL will
know when to stop reading.
115
Figure 6.1 Structure of molecule described in PCM file below.
116
PCM Example File
{PCM example pcm file
NA 31
SS 1cyclo pentadiene
FL EINT4 UV1 PIPL1
AT 1,8:5.00395,5.41685,4.14865 B 2,1 5,1 8,1 14,1 C .04109
AT 2,1:5.35786,3.99136,4.43375 B 1,1 3,1 15,1 16,1 C .04758
AT 3,3:3.89305,3.05742,4.72868 B 2,1 4,2 7,1 C .31634
AT 4,7:2.81165,3.08691,5.38735 B 3,2 6,9 17,1 18,1 C-.29483
AT 5,1:4.01102,5.78059,5.13175 B 1,1 6,1 19,1 20,1 C .00583
AT 6,Fe:3.37201,4.37477,5.09242 B 5,1 4,9 9,9 10,9 11,9 12,9 13,9 M3 R1.26000
C1.00000
AT 7,1:4.34527,1.64177,4.88598 B 3,1 21,1 22,1 23,1 C .04175
AT 8,23:5.80025,6.06569,4.07001 B 1,1 H C .15724
AT 9,48:2.72317,5.71177,3.69643 B 10,1 13,1 6,9 24,1 S, 1 P C-.03818
AT 10,2:2.74283,5.08259,2.49706 B 9,1 11,2 6,9 25,1 S, 1 P C-.03815
AT 11,2:2.37909,3.77508,2.58554 B 10,2 12,1 6,9 26,1 S, 1 P C-.03815
AT 12,2:2.02517,3.57846,4.02085 B 11,1 13,2 6,9 27,1 S, 1 P C-.03815
AT 13,2:2.22179,4.80733,4.59105 B 12,2 9,1 6,9 28,1 S, 1 P C-.03815
AT 14,20:4.70902,5.38735,3.60795 B 1,1 C-.21000
AT 15,5:5.98704,3.92254,5.39718 B 2,1
AT 16,5:5.92805,3.54897,3.55880 B 2,1
AT 17,20:2.37909,2.71334,4.92530 B 4,1 C-.05250
AT 18,20:2.75266,2.61503,5.84941 B 4,1 C-.05250
AT 19,5:3.46049,6.68504,4.76800 B 5,1
AT 20,5:4.51240,6.04603,6.10501 B 5,1
AT 21,5:3.51947,.88478,4.78767 B 7,1
AT 22,5:5.12192,1.35667,4.14865 B 7,1
AT 23,5:4.80733,1.51396,5.89856 B 7,1
AT 24,5:2.94928,6.78335,3.89305 B 9,1 S, 1 C .03818
AT 25,5:3.04759,5.59380,1.55329 B 10,1 S, 1 C .03815
AT 26,5:2.31027,3.01810,1.76957 B 11,1 S, 1 C .03815
AT 27,5:1.67126,2.64452,4.53206 B 12,1 S, 1 C .03815
AT 28,5:2.02517,5.05310,5.65279 B 13,1 S, 1 C .03815
AT 29,21:6.64571,6.42943,4.91547 B 30,1
AT 30,6:6.48842,6.06569,4.91547 B 29,1 31,1
AT 31,21:6.90132,5.87890,4.91547 B 30,1
}
The PCM file syntax or grammer is given below.
PCMFILE
--> (
{PCM [NAME(60)]
(ENTRY)
*
117
})
ENTRY
FIX_REC}
--> { SSNAME | ATOM_REC | NATOM | FLAGS | CONST |
SSNAME
--> SS [SP] NUM(16) [SP] [NAME(20)]
NATOM
--> NA NUM()
FLAGS
--> FL [SP] ({ PR | UV | EINT | PIPL } [NUM()] SP) *
CONST
--> CO {
ATOM_REC --> AT [SP] NUM() [SP] ATYPE SP X,Y,Z ([SP] ATFIELD)*
FIX_REC
--> FIX {
ATOM NUM() ( X Y Z ) |
DIS NUM() NUM() ( R FLOAT K FLOAT) }
ATYPE
--> { NUM(79) | NAME(2) }
X,Y,Z
--> FLOAT SP FLOAT SP FLOAT
ATFIELD
--> { BONDS | SUBSTR | ATOMFLG }
BONDS
--> B [SP] NUMBND SP (SP ATNUM,BNDORD )NUMBND
NUMBND
--> NUM(10)
ATNUM,BNDORD
--> NUM() (SP) NUM(10)
SUBSTR
--> S (NUM(16) SP)*
ATOMFLG --> FL { P | M NUM(3) | H | C FLOAT | R FLOAT } *
NAME(n)
--> letter{letter|digit|punc}* for size <= n
NUM(n)
--> {digit}
for value <= n
SP
--> {comma|blank|colon|tab}
FLOAT
-->
[-](digit)*[.](digit)(digit)*[{e|E}[{-|+}(digit)(digit)*]
letter
digit
--> character a-z A-Z $ _
--> character 0-9
{ } - choose exactly one: all choices separated by |
( ) - grouping: multiple tokens treated as one token
* - zero or more occurrences of previous token
[ ] - optional (one or zero occurences)
BOLD characters appear exactly
Starter token MUST appear in column one
ALL OPTIONAL SP NOTE: If the removal of an SP(space) from a string would place
two members of the same token primitive class adjacent, the SP is not optional!
118
16.2 MMX Input Files
It is a pleasure to acknowledge the contributions of Professor Allinger and his
students to the algorithms and constants used in MMX whose progenitors are MM2 and
the pi routines from MMP1.
PCMODEL can read:
A) a single structure file or
B) a file containing multiple but separate structure files.
For option B the first three characters on the first line of each new structure must be
MMX. This tag is used by PCMODEL to recognize the start of a new structure. Each
structure contains complete information about that structure.
The file format for an MMX and MM2 file are similar, differing only in the lack of a line
of logical variables to mark pi atoms in the MM2 file format. The file formats which
follow are for FORTRAN formatted files, that is column placement is critical if the file is
to be interpreted correctly. The format descriptors used in fortran are:
a#
character string of # length
i#
integer value up to # digits in size
f
fixed floating point number
Thus the format for line one (see below) says to read 30 fields of two character (30a2), a
series of integers that are 5 digits, 2, 3, 3, and 3 digits in length (i5,i2,i3,i3,i3) and a
floating point number that is 5 units wide with no number beyond the decimal point (ie
10. ). For a more complete description please see any Fortran programming guide. The
most important idea to remember is that data must be in specific columns in a fortran
formatted file.
First line:
columns
1-60
format (30a2, i5,i2,i3,i2,i3,f5.0)
61-65
N number of atoms including lone pairs.
67
IPRINT print control
ID name, title, or information
Initial Calculation Only:
0:
1:
2:
3:
4:
5:
Part 1-Minimize
minimum
minimum
full
simple
minimum
no print
0 or 1 simple; 2 or 3 full printout.
Part 3-Final
full
(can be 100+kb)
simple (useful)*
full
(can be 100+kb)
simple
minmum
(bare bones)
(Driver has its own out files)
119
* simple print omits VDW interactions <.1 kcal/mol
70
72
NRSTR
INIT
0:
0:
74
IDOCK docking — if zero then none — but MMX can provide other options
including simulated annealing of intermolecular interactions. These require the
beginning atom number for the substructure in the atom list. This number is on
NCON line (3rd line).
75
NCONST
0:
no restricted atom data
standard minimization
no added constants
1:
1:
1:
yes (see below)
initial calculation only
added constants
If NCONST = 1, added constants may be appended to input file — see below —
or in the form of a file which will be read if there are no input lines after the 13th
line as defined below. WARNING, if there are added constants, the use of the
multi coordinate input files will require that the added constants be in the input
file NOT in an external file.Since PCMODEL now uses a text file of added
constants this part of the MMX file format is not used.
76-80 time - ignored in all versions
Second line
1-60
format(60l1,i2,2x,i2,2x,2i2,4i1,2i2)
LOGARY: t or f in each column indicates whether or not the atom number
represented by the column number is to be considered a pi atom in a VESCF
calculation. If no atom numbers are marked t, no pi calculation will be
performed. If there are more than 60 atoms, add more lines with these logical
variables up to 4 lines total.
62 NPLANE 0:
planar pi calculation 1:
non planar
In a planar pi calculation, the first calculation is on a Huckel matrix whose
elements depend on the atom types and geometry Diagonalization gives a density
matrix which is used along with Slater orbital exponents and calculated overlap
integrals to give the elements of the FOCK matrix which is diagonalized to give a
new density matrix. Subsequent iterations give a self-consistent field with an
invariant energy.
In a non planar calculation two scf calculations are required-one on the
non planar system and one on a planar projection. The bond orders of the planar
projection are used to weight the natural distances, force constants, and two-fold
torsional barrier terms, see below (ADDED CONSTANTS).
66 JPRINT: print out for pi calculation
1st SCF
during minimization
120
0:
1:
2:
3:
energy only
energy + matrices
energy + matrices
ditto
energy only
energy only
energy + matrices on each iteration
energy + matrices on each iteration
69-70 LIMIT limit for self-consistency (10)-this integer (in ev). default is (10)-5
72
ITER maximum number of SCF iterations to be run. (ignored in this version with
open shell pi calculation)
73 IHBD
0:
1:
no read of hydrogen bonding logical array-all OH, NH, & SH hydrogens
participate in hydrogen bonding.
read hydrogen bond logical array after line 7 below; first line for 80
atoms; additional lines for up to total atoms; array marks which hydrogen
atoms will hydrogen bond.
74 ICOV
0:
1:
no metal atoms are present in input file
read line containing metal type and radius (3 different metals maximum)
then read logical array of atoms coordinated to each metal; lines must be
after the hydrogen bond array or after line 7.
75 IUV
0:
1:
2:
if pi calculation, MMX will ask for options before minimization:
number of electrons?
singlet, doublet, triplet, etc.?
RHF or UHF calculation?
if singlet, RHF then restrictions on wave function?
# of identical pairs of atoms?
atom numbers of pairs?
# of sets of identical bonds?
# of identical bonds and # of atom pairs?
default to singlet RHF pi calculation - no questions.
default doublet UHF pi calculation (for mono radicals) no questions.
76 IHUCK
0:
1:
for full VESCF calculation before first MM energy minimization
for Huckel calculation (of planar systems) before first MM; subsequent
minimizations will be full SCF
78 NSETAT - number of sets of equivalent pi atoms
121
80 NSETBD - number of sets of equivalent pi bonds
The previous two options are over-ridden by IUV greater then zero.
Then lines of logary (in 80l) for atoms beyond 60.
if NSETAT .gt. 0, must read ISETA(I) in 10i4, number of equivalent
atoms in each set; then must read nsetat lines in (20i4) which contain the atom
numbers in each set.
if NSETBD .gt. 0, must read ISETB(I) in 10i4, number of equivalent
bonds in each set; then must read lines in (20i4) which contain the atom numbers,
in pairs, for each bond. A new set must start a new line.
Third line
format(i5,1x,i1,2x,f5.1,5x,9i5,5X,2i5)
(if no pi atoms in molecule with more than 60 atoms — otherwise this is the 4th
line)
1-5 NCON # of connected atom lists (not atoms) to read in 30 Max.
7
IDYN
0:
1:
no dynamics
dynamics program is run interactively — After filename is given, user will
be asked:
Timestep in femtoseconds (1.0 fsec is default)
Viscosity in cp (0.000 is default)
Temperature of Bath (300.K is default, initial sample temperature is 300.K
so implies no heat in or out)
Time constant for heat transfer (1015 femtosecond is default, this implies
no coupling of bath to sample).
After 20 cycles, user can alter values and number of cycles. Dynamics can
be used to remove KE increasing the viscosity or cooling with a time constant ~
timestep so that an unstable structure can be optimized — slowly — invariably to
a local minimimum. At a given temperature kinetic and potential energy are
conserved an provide ranges of motion. A minimized structure can be heated to
escape a local minimum then cooled perhaps to a global minimum. Global
optimization can also be performed by minimizing many initial structures
generated by MODEL in MULTIC mode or PCMODEL in MULTOR mode - see
NDRIVE
11-15 DIELE dielectric constant.
If 0., default to 1.5.
122
If negative, a distance dependent dielectric constant is used in the chargecharge interactions (DIELC=Rij). If a negative dielectric is used with the dipoledipole calculations, nonsense will result.
16-20 JSTART atom number begining substructure in atom list-for docking onlyIDOCK of first line (col 74) must be set to >0.
25 IBUT
0: no
1: yes cyclopropropanes or cyclobutanes present
26-30 NATTCH # atoms attached to previously defined atoms.
31-35 NSYMM number of symmetry matrices to read in.
PCMODEL writes 0 for this variable.
36-40 NX number of coordinate replacement lines to read — this option is unnecessary
with structure file generation programs like MODEL, and PCMODEL. See
QCPE 395 documentation for its use. The coordinate replacement lines must
immediately follow the cartesian coordinate input.
45-50 LABEL
0:
names and weights of atoms defined in program are used.
#:
number of different atom types whose names and weights will be
changed below.
55 NDC
0:
dipole interaction enery will be calculated excluding interactions between
dipoles with a common carbon.
1:
as above but with all interactions.
2:
dipole interaction calculation supressed.
3:
charge interaction energy will be calculated (excluding interactions
between atoms bound to a common atom). If this option is used you must
read in atomic charges below.
4:
charge interaction energy used. Charges calculated from bond dipoles
with additions for pi atom charges.
PCMODEL writes 0 or 4 (default).
60 NCALC determines crystal conversion and/or orientations to be performed on input
coordinates.
0:
1:
2:
no crystal options.
input coordinates are reduced crystal coordinates. They will be converted
to cartesian coordinates (see below).
input coordinates will be oriented according to instructions below.
123
3:
Combination of 1 and 2 above.
65 HFORM
0:
no
1:
yes heat of formation calculated
2:
read new values for partition function contribution
formation.
to the heat of
80 NDRIVE
0:
no
1:
endocyclic dihd. driver
-1:
side chain dihd.driver
For options -1 and 1, a data line must be added before an added constants list at
the end of the input file. See below.
In MMX (a separate batch processing program) if NDRIVE >= 10000:
sets of coordinates can be read in after all other input. Each set must consist of
one line in format i5 which indicates the number of the set (starting from 1), and
the coordinates must be in the standard format (see SIXTH LINE below). The
previously read connectivity information will be used in the calculation. Files
with the filename + sequentially numbered extension will be generated. A brief
output file, *.SUM, with the filenames and energies will also be generated; an
energy ordered file MMXE.ORD is also generated.
In MMX: if NDRIVE=-9999:
global minimum finder by simulated
annealing. Requires additional input lines after the loghbd and logmet lines of
logicals.
OPTIONS FROM LINE ABOVE:
If LABEL _ 0 add # of LABEL lines in format (i5,3x,a2,f10.5)
4-5
ITY(i) atom type whose name and weight are to be redefined.
9-10
NAM(i) two character name for new atom type.
11-20 WGHT(i) Atomic weight for the atom.
If NDC = 3 add lines whose format is 8f10.5 listing the charge on each atom-for
N total atoms including lone pairs.
Fourth line(s) NCON lines each in format (16i5)
124
ICONN(i,j)
i=number of the line (1 to NCON), j=number of entry on line (from 2 to
16)
Each list contains up to 16 CONTIGUOUS atoms and each list can repeat atoms
in a previous list.
Cyclohexane would have one list with values 1,2,3,4,5,6,1
Bicyclo[3.2.1]octane would have two lists — the cyclohexane list above and a
second list with values 1,7,8,3
There are no restrictions on lists other than to avoid non contigous atoms during
the sequence.
Fifth line(s) NATTCH lines each in format (16i5)
number of lines sufficient to add all atom pairs up to NATTCH in format (16i5).
The pairs are:
JATTCH(i), KATTCH(i) where i equals 1 to NATTCH.
JATTCH(i)
is an atom already defined either in NCON or previously defined
as a KATTCH atom.
KATTCH(i) is an atom attached to JATTCH(i).
For cyclohexane NATTCH = 12 which would require two lines. The values are:
1,7,1,8,2,9,2,10,3,11,3,12,4,13,4,14
5,15,5,16,6,17,6,18
Sixth line(s) COORDINATES format(2(3f10.5,2i5))
1-10
X(1)
Coordinates in Angstroms of atom 1-These may be reduced crystal
coordinates if NCALC =1 or 3.
11-20
21-30
31-35
36-40
Y(1)
Z(1)
ITYPE(1) MMX atom type( see Table of Atom types)
MATOM(1)
36-38 atom number this atom is multiply bonded to.
39 (for metal atoms only
0:coordinately saturated;
1:unsaturated
2:>18 electrons
3:square planar).
40
Number of bonds to atom defined in 36-38 minus 1;
singly bonded to others will have matom = 00000
41-50 X(2)
125
Non metal atoms
51-60
61-70
71-75
76-80
Y(2)
Z(2)
ITYPE(2)
MATOM(2)
Repeat lines until all coordinates are included.
Seventh line(s)
NX > 0 COORDINATE REPLACEMENT or ATOM ADDITION
See documentation to QCPE 395 or QCPE MMP2(85) for options and data
structure.
Seventh line(s)
If NCALC = 1 or 3 CRYSTAL CONVERSION in format (6f10.5)
If reduced crystal coordinates were read in above instead of cartesians
coordinated, the following parameters will convert them to cartesian.
1-10
11-20
21-30
31-40
41-50
51-60
A
Dimensions of unit cell in Angstroms (a,b,c)
B
C
ALPHA Angles associated with unit cell.
BETA
GAMMA
Eighth line(s) Hydrogen Bonding flags
If IHBD=1 format(80l1). If N >80, more lines in format (80l1) are read.
These should be "f"s unless a particular hydrogen, whose atom number is
represented by the column number, will participate in hydrogen bonding-then a
"t" should be in the column.
Ninth line(s) If ICOV=1, Metal Names, Covalent Radii and Charge
Program checks number of metal atoms present (itypes 44,56,57) and
reads line of metal characters, covalent radii, and the charge on each metal
(necessary for isolated ions & might be useful for organometallics if electrostatics
are used) in format (3(a2,f8.6),9f5.2); these variables are
amet,rcova,bmet,rcovb,cmet,rcovc, and chrgmet(i), i=1,9. [Changing rcova will
change the covalent radius used for all bonds involving the metal amet.]
Then the number of metal logical lines of format(80l1) are read. A t or f
indicates whether or not the atom number represented by the column number is
coordinated (not bound as would appear in the NCON or NATTCH lists) to the
first (or second etc. 9 Max) metal atom in the atom number list.
If more than 80 atoms are present more lines should follow - in (80l1)
format-to mark the rest of the atoms.
126
Tenth line(s) If NSYMM .ne. 0 read NSYMM lines in format(2i4,9f8.5)
3-4
Is
number of the independent atom in the symmetry-related pair — it will be
moved during the minimization.
5-8
Ks
number of the dependent atom in the pair. Its coordinates are calculated
from a symmetry matrix operating on IS.
ELEMENTS OF SYMMETRY MATRIX - ON SAME LINE
9-16
17-24
25-32
33-40
41-48
49-56
57-64
65-72
73-80
SXX Amount by which X(K) must be changed when X(I) is moved by 1 Å in
order to maintain molecular symmetry.
SXY Change in Y(K) for X(I) change =1.
SXZ Change in Z(K) for X(I) change =1.
SYX Change in X(K) for Y(I) change =1.
SYY Change in Y(K) for Y(I) change =1.
SYZ Change in Z(K) for Y(I) change =1.
SZX Change in X(K) for Z(I) change =1.
SZY Change in Y(I) for Z(I) change =1.
SZZ Change in Z(K) for Z(I) change =1.
An atom may be used as Is as often as necessary but cannot appear in
another symmetry pair as Ks. In order to specify symmetry correctly, the
coordinate axes used in the minimization must be known. Do an initial calculation
with INIT=1.
This procedure is retained from MM2 but has not been tested in MMX.
Eleventh line(s)
Restricted atoms
If NRSTR =1 first line in format (i5) is number of atoms whose motions
are restricted, the remaining lines in format (16(i2,3i1) define the restrictions in
any or all of the X,Y, and/or Z directions. Thus the atom may be kept along an
axis, or in a plane, or at a point.
1-2
AT
Number of the atom whose motion is to be restricted.
3
4
5
X
Y
Z
0:
0:
0:
no restriction 1:
no X axis movement.
ditto 1:
no Y axis movement.
ditto 1:
no Z axis movement.
repeat up to 16 times per line.
Note that this will fail if the atom number to restrict is greater than 99.
127
This option is often considered for transition states, but its use is limited in
that connection. It is better to use transition state atoms whose constants can be
generated by PCMODEL.
Twelfth line if HFORM =2 read a line in format (3f5.2,f10.3)
1-5
POPI
population increment (Enthalpy contribution due to higher
energy conformations) Default=0
6-10
TORI
torsional increment (Enthalpy contribution due to torsional
degrees of freedom) Default=0
11-15 TROTItranslation-rotation increment (Enthalpy increment due to translational and
rotational degrees of freedom)
Default=2.4 kcal/mol.
21-30 Experimental heat of formation (kcal/mole)
31-40 Experimental error (absolute value)
41-80 Literature reference (optional)
Thirteenth line
Dihedral Driver Information
if NDRIVE is not equal to 0.
if NDRIVE < 10000 and NDRIVE .ne. -9999 in format(2(4i5,5x,3f5.0))
(Note that this line usually occurs at the end of an MM2 input file, but in MMX it
must preceed an added constants list which is appended to the input file.)
This is used to drive one or two dihedral angle(s) through a range of
values and to minimize all other degrees of freedom at each point.
1-5
6-10
11-15
16-20
26-30
31-35
36-40
41-45
46-50
51-55
56-60
66-70
71-75
76-80
M1
M2
M3
M4
atom numbers for first dihedral angle.
START1
starting angle
FIN1
final angle
DIFF1 step or increment
N1
N2
N3
N4
atom number for second dihedral angle.
START2
starting angle
FIN2
final angle
DIFF2 step or increment
128
Before use, remove restricted motions from atoms to be moved and
symmetry.
NDRIVE may be -1 for side chain or 1 for angles whose 2nd & 3rd atoms
are confined to rings.
The side chain driver is useful if the dihedral is not part of a ring. It
carries out a rigid rotation for each step in dihedral angle.
The endocyclic drive is confined within 0 and 180 degrees or 0 and -180.
The step cannot be large (5-10 degrees is normal). The minimization will stop if
either 0 or 180 degrees is achieved. Use the side chain driver if possible.
IF NDRIVE >= 10000 - see description for Third line above-requires
multiple sets of cartesians. MMX option only
IF NDRIVE = -9999 - Global minimization by simulated annealing. MMX
option only
1st line:
format 6i5
krbnds kring -0:
number of dihedrals to rotate, 30 MAX
no ring
1:
ring
irange for rings-angle window for closure usually 20 degrees
krand 0:
randomize all dihedrals before an energy check
(usual)
#:
randomize # dihedrals in the sequence below before
an energy check
igen - generating function type (use 0)
0:
15*temperature*(tan(pi*(ran-.5)) 0.<ran<1.
1:
360.*ran ntimes - Number of times structure with energy
within eminct is found before exiting (usually 4).
icomp normally zero, if
1:
read in three distances in line after dismin etc.
2:
for tricoordinate analysis - not thoroughly tested.
2nd line(s) format(16i5)
mbonds(kk,1),mbonds(kk,2),kk=1,krbnds : atom #s of bonds to rotate in
pairs If ring is chosen above, the first atom pair bond is broken and used for
evaluation closure distances and angles; the second atom pair should be an bond
adjacent to the first because it will be rotated in order to obtain the best closure
angle.
3rd line format(7f11.5)
129
dismin —
resln —
for ring - minimum distance between mbonds(1,1) and
mbonds(1,2) usually 1.50.
for ring - maximum distance between
" " " " " "
usually 1.58
dihedral angle to rotate through if igen = 0- usually 15
tempi —
initial temperature in kcal/mole usually 30.
codec —
decrement of temperature according to tempi*(1/(1.+ codec))
usually 0.5.
energy difference between acceptable structures to count for
minimum found ntimes in order (usually 0.01)..
dismax —
eminct —
4th line format(6f11.5) if icomp eq.2
3X (distance, tolerance) cdis1,tol1,cdis2,tol2,cdis3,tol3
Thirteenth line if IDOCK = 9
For simulated annealing in docking-main and substructure rigid-requires
that a substructure be at the end of the atoms list with the starting atom identified
in cols 16-20 on the third line (NCON and other options).
format(6f10.5,i5)
xyzds —
factor for substructure translation-usually 1.0
resln —
constant for substructure rotation-usually 15. degrees
tempi —
initial temperature-usually 3. kcal/mole
codec —
decrement of temperature according to tempi*(1/(1.+ codec))
usually 0.1
lowest temperature before quitting usually 0.01 kcal/mole
tempf —
eminct —
energy difference between acceptable structures to count for the
minimum if found ntimes in order (usually 0.2)
ntimes —
number of times a low energy is obtained to assume it is a
minimum usually 5.
ADDED CONSTANTS if NCONST .ne.0
This may be the last set of entries in the input file or may be a separate file which
MMX will read if this list is not at the end of the input file. PCMODEL will generate this
130
file only for transition state bonds. MODEL on the VAX will generate this file. The first
line is a header listing the numbers and types of constants to be read in format
(8i5,3f5.0,5x,f5.0,i5)
1-5
6-10
11-15
16-20
21-25
26-30
31-35
36-40
41-45
46-50
51-55
61-65
66-70
NT number of torsion parameter sets.
NS number of stretching parameter sets (includes bond dipoles).
NV number of van der Waals' parameters sets.
NB number of bending parameter sets.
MUA number of bond dipole line (according to type) - use NS.
MUB number of bond dipole lines (according to atom numbers) - use NS.
NSB
0: no
1: yet stretch-bend parmeters to be read.
NH number of bond enthalpy parameter sets-if NH_0, a heat of formation will be
calculated regardless of HFORM.(untested in MMX)
DLC new dielectric constant for dipole or charge interaction calculations-if
DLC=0, the default, 1.5 is used.
CST new cubic stretch term-default = -2.00
SF fraction of the bending constant that is to be used as sextic term in bending
energy equations-if SF=0, a default is used (7E-8).
RDN hydrogen vdw reduction factor-if RDN=0, the default is used (.915)- if
RDN=1, no reduction is used.
KTR number of transition state bond types.
next line
if NT > 0 TORSION CONSTANTS
- NT lines in format (4i5,3f10) from:
1 over 2 V sub 1 left ( 1 + cos OMEGA right ) + 1 over 2 V sub 2 left ( 1 - cos (2 OMEGA) right
) + 1 over 2 V sub 3 left ( 1 + cos ( 3 OMEGA ) right )
1
2-5
6-10
11-15
16-20
21-30
JBT
I1
I2
I3
I4
V1
31-40 V2
41-50 V3
4 for cyclobutane torsion 0 for all others
atom type numbers for dihedral; I2>I3 or if I2=I3, I1<I4
One-fold barrier; if >0, 0 deg is potential energy maximum, 180 deg is
potential energy minimum.
Two-fold barrier; if >0, 90 deg is potential energy maximum 0 and 180
deg are energy minima.
Three-fold barrier; if >0, 0 and 120 deg are energy maxima 60 and 180
deg are energy minima.
Note that ethylene has four torsional interactions making up the ca 60 kcal barrier so
V2=15 for type 2 - type 2 torsions. Ethane has six torsional interactions, etc.
131
next line
if NS > 0 STRETCHING CONSTANTS
— NS lines in format (2i5,6f10.5) from:
EC = 143.88*1/2ks*(1+CST*(r-r0))*(r-r0)2
E sub c = 143.88 * 1 over 2 k sub s left ( 1 + cst ( r - r sub 0 ) right ) cdot ( r - r sub 0 ) sup 2
where CST is cubic stretch term.
1-5
6-10
11-20
21-30
31-40
I atom type number
K atom type number; I .le. K
S stretching constant (ks above) in md/angstrom for bond I-K
T1 natural, minmum energy bond length (r0 above) in angstroms
T2 if I and K have one or less hydrogens attached T2 is the length used; if T2 is
zero T1 is used.
41-50 BMOM bond moment for pair I,K; if >0, K is more electronegative atom
51-60 SLPS for pi atom pairs: S = S-SLPS + SLPS * rhoI,K
61-70 SLPT for pi atom pairs: T1 = T1+SLPT - SLPT * rhoI,K Note that the
dipole-dipole interaction potential energy is:
Emu= 14.39418*BMOM(I,K)*BMOM(M,N)*(cos X - 3* cos A * cos B)/ DLC*r3
where r is the distance between the midpoint of the two bonds I-K and M-N;
X is the angle between the two bonds;
A is the angle between bond I-K and line represented by r;
B is the angle between bond M-N and line represented by r;
DLC is the dielectric constant whose default is 1.5. The dipole moment is
calculated from the vector sum of all bond moments. If a pi calculation is
performed, the dipole moment from the pi system is added vectorially to the
sigma dipole moment. There is presently no calculated interaction between the
pi and sigma dipoles.
next line
if MUA > 0 BOND DIPOLE CONSTANTS BY ATOM TYPE
MUA lines in format (2i5,f10.5)
4-5
I
6-10 k
11-20 BMOM
atom type number
atom type number; I _ K
bond moment for pair I,K; if >0, K is more electronegative atom
It is more consistent to change the BMOM in the added Stretch constants since all six
values are read from the data base.
next line
if MUB > 0 BOND DIPOLE CONSTANTS BY ATOM NUMBER
132
MUB lines in format (2i5,f10.5)
4-5
N1
9-10 N2
11-20 V12
atom number of the less electronegative atom
atom number of the more electronegative atom
new bond moment for bond N1-N2. V12 should be negative if N1 is more
electronegative than N2.
(untested in MMX)
next line
if NV > 0 VAN DER WAALS' CONSTANTS
NV lines in format (i10,2f10.5)
EV = eps*290000*e-12.5/p - 2.25*p6
where p = (RDi+RDk)/r0 < 3.311
eps = sqrt(EPi*EPk) "hardness"
r0 effective distance (for CH bonds the H is effectively 10% closer to the
C than the actual C-H distance).
EV = eps*336.176*p2 if p > 3.311
9-10 IT atom type number whose parameters are to be changed
11-20 EP epsilon (kcal/mole) for type IT atom
21-30 RD radius in angstroms for type IT atom
The user has no control over the parameters used for hydrogen bonding
and coordination to a metal. These are included in the vdw parameters because
the vdw attractive term for hydrogen bonding and for the lone pair or pi atom
interaction with a metal is proportional to p2 not p6. The attractive are much
larger than 2.25, depend on the donor and acceptor and angles, and is matched by
a larger repulsive term.
next line
if NB > 0 BENDING CONSTANTS
NB lines in format (i1,i4,2i5,2f10.5,i5)
from:
EB = 0.043828*1/2*kb*((theta0-theta)2)*(1+SF*(theta0-theta)4)
1
2-5
where SF is sextic bending constant (.00700E-5).
JBN
3 for cyclopropane angle
4 for cyclobutane angle
I1
atom type number; I1<I3; if I1 is -1 read OPB constants where I3 is the
central atom which is OP.
133
9-10
11-15
21-30
31-40
45
I2
I3
B
T
J
atom type number
atom type number
bending constant (kb from above)
natural, minimum potential energy bond angle in degrees (theta)
0: T value applies to all I1-I2-I3 angles
1: T value applies only if I2 has no attached hydrogens
2: T value applies only if I2 has one attached hydrogen
3: T value applies only if I2 has two attached hydrogens.
Out of Plane bending (OPB): trigonal atoms involved in out of plane bending have an
in-plane component, which is characterized by the standard values from above, and an
out of plane component with a different constant. The atom types which respond to
OPB constants are types 2 (SP2C), 3 (carbonyl C), 9 (amide and pyrrole nitrogen), 29
(carbon radical), 30 (carbocation), and 48 (carbanion when it is a pi atom). The default
values for these are similar to that in MM2 for type 3 namely: 0.8.
next line
if NSB > 0 STRETCH-BEND CONSTANTS
NSB lines in format (4f10.5) from:
ESB = 2.51118 * ksb * theta * (r1,2 + r2,3)
where ksb are constants described below;
theta is angle 1-2-3;
r1,2 is distance between atoms 1 and 2;
r2,3 is distance between atoms 2 and 3.
1-10
SB1
constant for angle a-f-c where f is a 1st row atom; a and c are any
non-hydrogen atoms. Both bonds are considered in ESB. Default value is
0.12.
11-20 SB2 constant for angle a-s-b where s is a 2nd row atom; a and c are any
non-hydrogen atomsDefault value is 0.25.
21-30 SB1H constant for angle a-f-H where f is a 1st row atom; a is any non-hydrogen
atom; only bond a-f is considered in ESB. Default value is 0.09.
31-40 SB2H constant for angle a-s-H where s is a 2nd rwo atom; a is any non-hydrogen
atom; only bond a-s is considered in ESB Default value is -0.40
next line
if NH > 0
HEAT OF FORMATION BOND AND STRUCTURAL PARAMETERS
NH lines of format (2i5,2f10.5,i5,5x,5a4)
1-5
6-10
11-20
21-30
IT
KT
BE
SBE
atom type number defining a bond or structural feature number
atom type number defining a bond (zero if structural feature)
bond enthalpy increment for IT-KT bond or structural feature
bond entropy increment for IT-KT bond (zero if structural)
134
35
NEW
0: Default comment on bond enthalpy (use zero if structural)
1: change or add comment on bond enthalpy
41-60 NTITLE
Comment on bond enthalpy (ignore if structural)
16.3 Mopac and Ampac Files
Mopac input and output files are 'free format' internal coordinate or cartesian
files. The free format refers to the fact that data may be entered at any position on a line,
there is no fixed column number in which the data must appear to be read correctly. The
internal coordinate format consists of lists of bond lengths, angles and dihedrals and the
defining atoms which describe the molecular geometry, as opposed to a list of cartesian
coordinates for all the atoms. In internal format for any atom (i) there is an interatomic
distance in Angstroms from an already defined atom (j), and interatomic angle in degrees
between atoms i and j and a previously defined atom (k), where j and k are different, and
a dihedral angle in degrees between atoms j,k and a previously defined atom (l), where l
is different from j and k. Atom 1 has no coordinates since this is defined as the origin,
atom 2 is connected to atom 1 by an interatomic distance only, and atom 3 is connected to
atom 1 or atom 2 by an interatomic distance and makes an angle (either 3-1-2 or 3-2-1)
with no dihedral angle defined.
A mopac file for benzene is given below :
am1
C
C
C
C
C
C
H
H
H
H
H
H
0.000000
1.400211
1.399883
1.400132
1.399876
1.400199
1.103109
1.103110
1.103109
1.103109
1.103109
1.103109
0
1
1
1
1
1
1
1
1
1
1
1
0.000000
0.000000
119.996750
120.005653
119.993233
120.006828
119.998314
120.002739
119.998428
120.002640
119.997231
120.001671
0
0.000000 0 0 0 0
0
0.000000 0 1 0 0
1
0.000000 0 2 1 0
1
0.000000 1 3 2 1
1
0.000000 1 4 3 2
1
0.000000 1 5 4 3
1 180.000000 1 1 2 3
1 180.000000 1 2 3 1
1
0.000000 1 3 2 2
1
0.000000 1 4 3 3
1
0.000000 1 5 4 4
1
0.000000 1 6 5 5
line 1: keywords separated by one or more spaces such as : am1
line 2: title line up to 60 characters long:
blank
line 3: second title or comment line up to sixty atoms long: blank
line 4 to end :
Atom Symbol Dist Opt Angle Opt Dihed Opt NA
NB
135
NC
The atom symbol is the atomic symbol for that atom. The distance is the interatomic
distance between the current atom and the atom number given in the NA column. Thus
atom 2 is referenced to atom 1, atom 7 (which is a hydrogen) is reference to atom 1 also.
The Opt columns determine whether this parameter (distance, angle or dihedral) will be
optimized by Mopac, with a 1 to optimize and a 0 to not optimize. The angle is the angle
formed by the current atom and the atoms NA and NB. Thus atom 4 is referenced to atom
3 for the distance and makes the angle of 120.005 with atoms 3 and 2 ( angle 4-3-2). The
dihedral angle is defined for atoms 4-3-2-1 to be 0.0 degrees.
For a more complete description of Mopac files and options please see the
MOPAC documentation which is available from QCPE or from Serena Software.
16.4 X-RAY Files
Since there is no universally accepted file format for x-ray data, we have written a
free format file parser that should allow you to input the data in any format. Our routines
expect:
Line 1:
Title
character string of up to 80 characters
Line 2:
Cell Parameters
A,B,C,Alpha, Beta and Gamma
Line 3 to end: X,Y,Z coordinates and atom symbol.
Note that these routines do not read symmetry matrices or point groups. Thus we assume
the coordinates are orthogonal and that the cell paramters are floating point numbers
(including the decimal point). If you understand this then you probably have the
necessary programs to output this type of data. A sample x-ray input file is included
below. A set of dummy cell parameters to use with a set of Cartesian coordinates would
be: 1. 1. 1. 90. 90. 90. (note you need the decimal point, all the cell parameters are
read as real numbers).
Test input file
1.0 1.0 1.0 90.0 90.0 90.0
0.124381 -0.144487 -0.435695
-1.526023 0.158658 0.185498
0.818900 1.213381 0.125534
0.638991 -1.256924 0.361156
-1.905993 1.082317 -0.230632
-2.152138 -0.671798 -0.115534
-1.491980 0.209408 1.267034
1.053019 1.088258 1.043743
s
c
o
o
h
h
h
h
136
16.5 SDF and Mdl Mol Files
16.6 Chem3D and Tinker Files
16.7 Cambridge Structural Database Files
16.8 Alchemy and Sybyl Mol Files
16.9 Gaussian Input and Output Files
16.10 Gamess Input and Output Files
16.11 ADF, PQS, Hondo and Turbomole Files
16.12 Smiles Files
137
Chapter 17 Parameter Files
All of the parameters, constants and atom type definitions for a given force field
are defined in a text file. The format of this file is similar to that developed by Professor
Jay Ponder of Washington University for the Tinker program. The files currently
distributed with Pcmodel are:
Mmxconst.prm
Mm3.prm
Mmff94.prm
Amber.prm
Oplsaa.prm
Parameter file for MMX force field
Parameter file for Allinger’s MM3 force field
Parameter file for Halgren’s MMFF94 force field
17.1 Overview
All the parameter files include a definition of the constants used for the various
energy equations used by that force field, the atom types defined and the parameters
required. The file is free format and data lines begin with a keyword that starts in column
one followed by the data separated by one or more spaces. The information can be
defined in any order since each line is parsed and interpreted. The beginning of the MMX
force field parameter file is given below.
MMX (1986)
##############################
##
##
## Force Field Definition
##
##
##
##############################
forcefield
MMX
bondunit
bond-cubic
bond-quartic
angleunit
angle-sextic
str-bndunit
torsionunit
vdwtype
radiusrule
radiustype
radiussize
epsilonrule
atom-14-scale
a-expterm
b-expterm
c-expterm
chg-14-scale
dielectric
71.94
-2.0
2.333333
!! (7/12) * bond-cubic^2
0.02191418
0.00000007
2.51118
0.5
BUCKINGHAM
ARITHMETIC
R-MIN
RADIUS
GEOMETRIC
1.0
290000.0
12.5
2.25
1.0
1.5
Definitions for some of the keywords are:
Forcefield
definition of the name of the forcefield
138
Bond_unit
Bond_cubic
Vdwtype
Radiusrule
Dielectric
constant for converting bond constants to energy
same as above or zero if cubic stretch not used
Definition of vdw equation to use, Buckingham or Lennard-Jones
combining rule for vdw radius
default dielectric constant
17.2 Atom Types
Atom type definitions begin with the keyword ‘atom’, followed by a numeric
atom type, character atom type, a twenty character text description, atomic number,
atomic weight, number of bonds, total bond order, and the atom class definition. In the
example from MMX given below the first four atom types defined are all carbon, with
atom type 1 being an sp3 carbon that forms four bonds, atom types 2 and 3 being sp2
carbons that form three bonds and finally atom type 4 which is a sp carbon and only
forms two bonds. The information about bonds is necessary to automatically add
hydrogen to an atom. The atom class definition allows the users to create many specific
atom types without having to provide complete data for all of them. For example, MM3
defines the basic carbonyl oxygen as type 7 and then defines atom types 77 to 101 as
specific types of carbonyls. In the data set there are specific stretching force constants for
many of the carbonyl atom types, but if data is missing the default type 7 parameters are
used.
##
atom
atom
atom
atom
atom
atom
atom
atom
atom
Atom Types
1
2
3
4
5
6
7
8
9
C
C
C
C
H
O
O
N
N
CSP3
CSP2 ALKENE
CSP2 CARBONYL
CSP ACETYLENE
HYDROGEN
C-O-H, C-O-C
=O
CARBONYL
NSP3
NSP2
6
6
6
6
1
8
8
7
7
12.011
12.011
12.011
12.011
1.008
15.999
15.999
14.007
14.007
4
3
3
2
1
2
1
3
3
4
4
4
4
1
2
2
3
3
1
2
3
4
5
6
7
8
9
17.3 Bonds
The bond stretching function used in Pcmodel is a fourth order polynomial. Force
fields such as Amber and Oplsaa are supported by setting the cubic stretch and quartic
stretch terms to zero, while MM2, MM3, MMX and MMFF94 are supported by defining
these terms.
Es = bu*ks/2*(δr)2 *[1 – cs*( δr) + qs*(δr)2]
Where:
Bu
Ks
Dr
Cs
bondunit , conversion factor from md/A2 to kcal/mol-A2
stretching force constant
actual bond length – defined bond length
cubic stretching term defined in parameter file
139
Qs
quartic stretching term defined in parameter file
The keywords used for defining the bond parameters (force constant and defined
bond length) are Bond, Bond3, Bond4, Bond5 and Bonddel. Parameter data begins with a
keyword followed by the two atom types comprising the bond with the lower numbered
atom type first. Next comes the stretching force constant and the defined bond length.
The bonddel keyword only applies to MMFF94 and is used for bonds that are part of
conjugated pi systems. Since MMFF94 does not support pi calculations it deals with
delocalization by explicitly recognizing delocalized systems and using bond , angle and
torsion parameters appropriate for this type of system. Thus the central bond of butadiene
would be treated with a bonddel parameter for a type 2-type 2 bond. Examples of bond
parameters are given below.
bond
bond3
bond4
bond5
bonddel
1
5
6
1
2
1
22
56
1
2
4.4900
5.130
5.7000
4.4900
5.3100
1.5247
1.0860
1.4250
1.5258
1.4300
17.4 Angles
Pcmodel uses both in-plane and out-of-plane bending functions. The in-plane
angle deformation function used is a sixth order polynomial in delta theta. Force fields
such as Amber and Oplsaa use only the harmonic term while MMX, MM2, MM3 and
MMFF94 use the higher order terms.
Eb = au*kb/2*(δΘ)2*[1 + cf*( δΘ) + qf*( δΘ) 2 + pf*( δΘ)3 + sf*( δΘ)4]
Where:
conversion factor from md A/rad2 mol to kcal/deg2 mole
bending force constant
actual bond angle – defined bond angle
cubic angle bending constant
quartic angle bending constant
pentic angle bending constant
sextic angle bending constant
Au
Kb
δΘ
Cf
Qf
Pf
Sf
The keyword used for defining the in-plane angle parameters (bending force
constant and defined angle) are angle, angle3, angle4, angle5 and angldel (MMFF94
only). Parameter data begins with a keyword followed by the three atom types of the
atoms comprising the angle, the bending force constant and up to three defined angles.
The first angle given is the default value and the value used if no hydrogens are attached
to the central atom. If a second angle is present and not zero, it is used for angles with
one hydrogen attached to the central atom. If a third angle term is present and not zero it
is used for angles with two hydrogens attached to the central atom. Examples of angle
parameters are given below.
angle
angle3
angle4
angle5
1
22
1
1
1
19
1
1
1
22
9
1
0.6700
0.1250
0.5500
0.6700
109.5000
50.2000
106.5000
109.5000
140
110.2000
0.0000
0.0000
109.9000
111.0000
0.0000
0.0000
111.0000
angdel
1
2
63
0.7680
127.9450
Pcmodel has two out-of-plane bending functions which are applied to sp2 atom
types. The standard Allinger implementation uses the angles defined by the projection of
the central atom onto the plane defined by the three attached atoms. MMFF94 uses the
Wilson angles to define the out of plane deformation. The keyword is opbend and is
followed by four atom types in the order of attached atom, central atom, attached atom,
attached atom. The Allinger type implementations use only the second and third atom
types (the first and fourth can be set to zero), while MMFF94 requires that all four atom
types be defined.
opbend
opbend
0
1
2
2
1
1
0
2
0.1000
0.0300
(MMFF94)
17.5 Stretch-Bend
The stretch-bend potential function is:
Esb = ksb*(δΘ)*(δr)
The keyword is strbnd and it is followed by the three atom types of the atoms defining
the angle and three force constants. The force constants are ordered by the number of
hydrogens attached to the central atom and the order is zero, one and two.
strbnd
strbnd
0
1
1
1
0
1
0.130
0.2060
0.080
0.2060
0.000
0.000
0
MM3
MMFF94
17.6 Torsions
The torsion potential function is a six term fourier series in the cosine of the
dihedral angle.
Et = V1/2*(1+cosφ) + V2/2*(1-cos2φ) + V3/2*(1+cos3φ) + V4/2*(1-cos4φ) +
V5/2*(1+cos5φ) + V6/2*(1-cos6φ)
The Allinger based force fields, such as MM2, MMX and MM3, and MMFF94 use the
first three terms of the series, while the harmonic force fields, such as Oplsaa and Amber,
use only one of the first three terms. The keywords are torsion, torsion4, torsion5 and
torsiondel, followed by the four atom types of the dihedral angle, the force constant and
then the phase for that force constant.
torsion
torsion5
torsion4
torsiondel
1
1
3
2
1
1
1
5
1
1
1
1
1
1
9
2
2
141
0.185 +1
0.185 +1
0.000 +1
0.0000 +1
0.170 -2
0.170 -2
0.000 -2
0.0000 -2
0.520 +3
1.160 +3
0.250 +3
0.0550 +3
17.7 Van der Waals
There are three different vdw functions programmed in Pcmodel. The
Buckingham potential used by the Allinger force fields, the Leonard-Jones potential used
by Amber and Oplsaa, and the buffered-7-14 potential used by MMFF94.
Lennard-Jones
Buckingham
MMFF94
Evdw = 4E*(( A/r)12 -( B/r)6)
Evdw = A' exp( -B ' /r) -( C/r ) 6
Evdw = 4E*(( A/(r+const))14 -( B/(r+const))7)
The keywords are vdw, vdwpr and vdwmmff. The vdw keyword is used for basic
vdw parameters and is followed by the atom type, the vdw radius and epsilon. The A, B
and C constants are defined in the part of the parameter file dealing with general force
field constants as are the combining rules. The MMX and MM3 force fields have
separate entries for special pairs of atoms and this is done with the keyword vdwpr
which is followed by two atom types the vdw radius and epsilon. This is primarily done
for C-H interactions, but can also be used to describe other types of non-bonded
interactions, such as that between metal ions and pi systems. The MMFF94 parameters
are taken directly from Halgren’s published set of parameters and the vdw interactions
are computed as given in “Merck Molecular Force Field.II. MMFF-94 van der Waals and
Electrostatic Parameters for Intermolecular Interactions”, J Comp Chem, 17, 520-552
(1996).
vdw
vdwpr
vdwmmff
1
1
1
2.040
3.560
1.0500
5
0.027
0.023
2.4900
3.8900
1.2820
-
17.8 Charge and Dipole
Pcmodel implements a coulomb potential function, charge-dipole and dipoledipole potential functions. In the MMX force field charges are computed from the bond
dipole moments. In MM3 the dipole moments are used directly in charge-dipole and
dipole-dipole calculations. MMFF94 charges are computed as given in the J Comp Chem
reference. In Amber the charges are entered directly in the parameter file and are taken
from the Amber-95 JACS paper. For Oplsaa atom type charges are based on the chemical
environment as encoded in a Smiles string, but if no charge is found in the parameter file
MMFF94 charges are used. The keywords are dipole, charge, mmffcharge and bndchrg .
dipole
charge
mmffchrg
bndchrg
1
30
1
1
2
1
0.9000
1.000
0.0000
0.0000
0.0000
0.0000
E94
#C94
17.9 MM3 Specific
angang
strtors
electroi
1
1
1
1
1001
3
0.240
0.059
-0.007
142
0.300
0.000
17.10 Pi Calculations
MMX and MM3 use a PPP type scf calculation to modify the bond stretching and
torsion parameters for pi systems. The pibond keyword is followed by two atom types,
the bond stretching force constant, the bond length for a full pi bond, the bond moment
(which is no longer used), the rate of change of the force constant with pi bond order and
the rate of change of the bond length with pi bond order. The equations for modifying the
pi bond length and force constant are:
Force_constant = bkon - slpk + slpk*pbo;
Bond_length = blen + slpl - slpl*pbo;
Where :
Pbo
Bkon
Slpk
Blen
Slpl
piatom
pibond
pi bond order
force constant from parameter file
change in force constant with pi bond order
bond length from parameter file
change in bond length with pi bond order
2
2
1.0
2
-11.160
7.5000
11.134 3.25
1.3320
0.0000
143
3.25
0.841
5.486
2.8200
0.1700
-15.172
4

PCMODEL V 9.0

Transcription

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