MOPAC Guide

MOPAC Guide
Schrdinger Suite 2009

Schrdinger Press

MOPAC Guide Copyright 2009 Schrdinger, LLC. All rights reserved.

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Revision A, October 2009

Document Conventions

In addition to the use of italics for names of documents, the font conventions that are used in
this document are summarized in the table below.
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Sans serif

Project Table

Names of GUI features, such as panels, menus,

menu items, buttons, and labels

Monospace

$SCHRODINGER/maestro

File names, directory names, commands, environment variables, and screen output

Italic

filename

Text that the user must replace with a value

Sans serif
uppercase

CTRL+H

Keyboard keys

Links to other locations in the current document or to other PDF documents are colored like
this: Document Conventions.
In descriptions of command syntax, the following UNIX conventions are used: braces { }
enclose a choice of required items, square brackets [ ] enclose optional items, and the bar
symbol | separates items in a list from which one item must be chosen. Lines of command
syntax that wrap should be interpreted as a single command.
File name, path, and environment variable syntax is generally given with the UNIX conventions. To obtain the Windows conventions, replace the forward slash / with the backslash \ in
path or directory names, and replace the $ at the beginning of an environment variable with a
% at each end. For example, $SCHRODINGER/maestro becomes %SCHRODINGER%\maestro.
In this document, to type text means to type the required text in the specified location, and to
enter text means to type the required text, then press the ENTER key.
References to literature sources are given in square brackets, like this: [10].

MOPAC Guide

Schrdinger Suite 2009

MOPAC Guide

MOPAC in Schrdinger Suite 2009

Schrdinger Suite 2009 provides access to the basic semi-empirical capabilities of MOPAC
through a library installed with mmshare. This library is based on MOPAC 7.1, which was
obtained from http://openmopac.net. Although the complete MOPAC 7.1 source was used to
create this library, only a small part of it has been validated. At this time, the module may be
used to calculate semi-empirical heats of formation, optimized geometries, force constants,
and a few properties as indicated below. MOPAC can be run from Maestro or from the
command line. A manual for MOPAC 6 is available on request from help@schrodinger.com
but we do not have access to a manual for MOPAC 7.1, nor are we aware of any release notes
that describe the changes between MOPAC 6 and MOPAC 7.1.
Note:

The version of MOPAC provided here is not the commercial version: it is the opensource version. Its capabilities are therefore not the same as the commercial version.

The MOPAC Panel

MOPAC jobs can be set up and run from Maestro by using the MOPAC panel. To open this
panel, choose Applications > MOPAC in the main window.
The input structures can come from a file, or from the Project Table or the Workspace. You can
choose the structure source from the Use structures from option menu. If the input structure
source is a file, enter the file name in the Input file text box, or click the Browse button and
navigate to the input file. The structure file can be in Maestro, SD, or MOL2 format.

Figure 1. The MOPAC panel.

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MOPAC in Schrdinger Suite 2009

You can choose the method to use from the Method option menu. The available methods are
RM1, AM1, PM3, MNDO and MNDO/d. If you want to optimize the geometry, select Optimize geometry; otherwise a single-point calculation will be run. To specify options other than
the method, you can enter keywords in the MOPAC keywords text box. The keywords you can
use are described under Supported Keywords.
In addition to a Maestro file, the output from the job includes the MOPAC output files for each
structure. You can collect these files into a zip file by selecting Archive MOPAC output files.
To start the job, click Start, make settings in the Start dialog box, then click Start. You can
choose not to incorporate the results into the Maestro project, or to append new entries to the
project. The output properties include the semiempirical energy as an entry property, and the
atomic partial charges as atom-level properties.

Running a MOPAC Job from the Command Line

To run a MOPAC job from the command line, use the following syntax:
$SCHRODINGER/run mopac.py [options] [job-options] structure-file
The input structure file can contain multiple structures, which will all be processed in the job.
The file can be in Maestro, SD, or MOL2 format. The command options are given in Table 1.
Table 1. Options for the mopac.py command

Option

Description

-v[ersion]

Show the program version and exit.

-h[elp]

Show usage message and exit.

-geopt

Run a geometry optimization. This is the default.

-nogeopt

Dont run a geometry optimization.

-method method

Specify the method to be used. Choices are AM1, MNDO, MNDO-d, PM3,
RM1. Default: RM1.

-mopac_opts options

Specify a string that contains additional MOPAC keywords.

-j[obname] jobname

Specify a jobname for .log and .out files. Can only be used with single input files.

-no_out

Dont save the MOPAC .out files, leaving only the output structures.

-zip_out

Create a .zip file with all MOPAC .out files

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MOPAC in Schrdinger Suite 2009

Table 1. Options for the mopac.py command

Option

Description

Job Control Options:

-HOST host

Run job remotely on the indicated host entry.

-WAIT

Do not return control to the shell until the job finishes.

-DEBUG

Show details of Job Control operation.

-SAVE

Return zip archive of job directory at job completion.

-NOJOBID

Run the job directly, without Job Control layer.

As an example, if you have a multi-structure Maestro file called myfile.mae that contains
three ligands whose geometries you would like to optimize with the PM3 method, and you also
want to print out the final bond order matrix, and the sigma-pi bond order matrix, you would
use this command:
$SCHRODINGER/run mopac.py -method pm3 -mopac_opts "bonds pi"
myfile.mae
This job produces files named myfile_1.out, myfile_2.out, and myfile_3.out, which
contain the MOPAC output, together with an output structure file called myfile_out.mae,
which contains the final geometries, the method used, the semi-empirical energy, and the
atomic charges (which are calculated by default). This structure file may be manually imported
into Maestro. Atoms may be labeled with their partial charges by selecting Atomic Charge
from the list of available labels in the Atom Labels panel. These charges may also be used in
docking calculations with Glide. In addition, a log file is produced, which includes information
about the job options used.
It is possible to use a native MOPAC input (.dat or .mop) file as well, but this capability is
intended only for users who are already familiar with MOPAC and are therefore less dependent
upon the existence of a manual that describes all supported keywords in detail. The MOPAC
input file is expected to already contain all of the desired keywords, and the -geopt,
nogeopt, -method, and -mopac_opts command-line options are not allowed in this case.
The Job Control command-line options are still supported, however.

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MOPAC in Schrdinger Suite 2009

Supported Keywords
The keywords that are supported for use with the -mopac_opts command option are given in
this section. Keywords are not case-sensitive.

General Keywords
RM1, AM1, PM3, MNDO, MNDOD
These keywords select the method used to calculate the semi-empirical heat of formation. RM1
is the default, and is recommended. It is a reparameterization for some of the elements covered
by AM1. MOPAC automatically uses AM1 parameters for elements covered by AM1 that are
not covered by RM1. The elements covered by the methods as they are implemented in
MOPAC 7.1 are given in Table 2.
Table 2. List of elements covered by MOPAC methods.
Method

Elements covered

RM1

H, C, N, O, F, P, S, Cl, Br, I

AM1

H, B, C, N, O, F, Al, Si, P, S, Cl, Zn, Ge, As, Se, Br, Sb, Te, I, La, Ce, Pr, Nd, Pm,
Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu, Hg

PM3

H, Li, Be, C, N, O, F, Na, Mg, Al, Si, P, S, Cl, Zn, Ga, Ge, As, Se, Br, Cd, In, Sn,
Te, I, Hg, Tl, Pb, Bi

MNDO

H, Li, Be, B, C, N, O, F, Na, Al, Si, P, S, Cl, K, Zn, Ge, Br, Sn, I, Hg, Pb

MNDOD

Na, Mg, Al, Si, P, S, Cl, Zn, Br, Cd, I, Hg

The literature citations for the sources of parameters for these elements is printed by the
program when the parameters are used, so please consult the output file for this information.
CHARGE=n
For charged molecules, CHARGE must be set to the overall molecular charge.
DOUBLET, TRIPLET, QUARTET, QUINTET, SEXTET, SEPTET
MOPAC assumes singlet spin multiplicity. When modeling radicals of higher spin multiplicity,
set the appropriate keyword from the above list. Multiplicities higher than SEPTET cannot be
handled by MOPAC 7.1.

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MOPAC in Schrdinger Suite 2009

MMOK, NOMM
One of these two keywords must be set whenever a calculation is performed on a molecule
containing a peptide bond. For the convenience of batch processing large numbers of structures, MMOK is set by default, and is ignored for molecules that do not contain a peptide bond.
With MMOK set, MOPAC applies a correction factor (derived from molecular mechanics) to
the rotational barrier around each peptide bond. This is to compensate for the fact that all of the
NDDO methods in MOPAC 7.1 underestimate this rotational barrier. To prevent this correction
from being applied, set NOMM.
FORCE, THERMO(nnn,mmm,lll)
The FORCE keyword causes MOPAC to calculate the vibrational frequencies for the input
molecule. The THERMO keyword, without any of the optional arguments in parentheses,
causes MOPAC to calculate the thermodynamic properties such as internal energy, enthalpy,
and entropy, plus the vibrational, rotational, translational partition functions. By default, the
thermodynamic functions are calculated at 298K and at 10K increments from 200K to 400K. A
different starting temperature, final temperature, and increment can be specified using the
(nnn,mmm,lll) options. For example, use THERMO(273,293,20) to print thermodynamic
properties at 298K (which is always done) and at 273K and 293K.

Molecular Properties
MULLIK
By default, MOPAC prints the atomic charges by summing up the density matrix elements for
each atoms basis functions. To take into account the overlap of basis functions between atoms,
use this keyword to perform a Mulliken analysis.
ESP
Print the atomic charges that best reproduce the molecular electrostatic potential.
BONDS
Print the bond orders for all pairs of atoms.
PI
Print bond orders broken down into sigma and pi components.
SUPER
Print the nucleophilic (Dn(r)) and electrophilic (De(r)) delocalizabilities, superdelocalizabilities
(piS(r)), electronegativity, absolute hardness, Schuurman MO shift alpha values, and the
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MOPAC in Schrdinger Suite 2009

percentage that each atomic orbital (excluding hydrogens) makes to the frontier molecular
orbitals.
VECTORS
Print the coefficients, energies, and symmetries for the molecular orbitals near the HOMO and
LUMO.

Troubleshooting
If you use a Maestro structure file as input, and you experience a problem running MOPAC and
want to see the MOPAC input file that is created from the .mae file, include the -SAVE option
on the command line. This option creates a .zip file of the job scratch directory, including the
MOPAC input file, which has the name jobname.mop. You might be able to edit this file to
work around the problem, and then submit the job using the .mop file as input. See Known
Limitations for information on conditions that could cause failure.

Known Limitations
Some known limitations are listed in this section.

Diatomic and triatomic molecules

Diatomic and triatomic molecules must be input using internal coordinates. If cartesian coordinates are used, MOPAC often prints a warning that two atoms are too close, which is due to an
erroneous handling of the input. Since Maestro structure files cannot use internal coordinates,
the only solution in this case is to use a text editor to create a native MOPAC input file and
supply internal coordinates to describe the molecular structure.
Internal coordinates may be specified in Z-matrix format, in which each atoms position is
related to previous atoms by a bond distance, an angle, and a dihedral angle. References to
previous atoms must be made using their index numbers, that is, the first atom in the input is
atom 1, the second atom is atom 2, and so forth. The format of a Z-matrix is as follows:

10

Column 1:
Column 2:
Column 3:
Column 4:
Column 5:
Column 6:
Column 7:

The atomic symbol. No trailing index numbers are allowed

The index number of a previous atom
The distance, in angstroms, from a previous atom, or a variable name
Another atom index number
An angle, in degrees, or a variable name
Another atom index number
A dihedral angle, in degrees, or a variable name

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MOPAC in Schrdinger Suite 2009

If variables are used, they are defined below the Z-matrix, after a single blank line. Here is an
example of a Z-matrix for formic acid:
C
O
H
O
H

1
1
1
4

r2
r3
a3
r4
a4
d4
r5
a5
d5

1.2
1.1
120
1.3
119
180
0.95
106.1
0

r2
r3
r4
r5

2
3
1

a3
a4
a5

2
3

d4
d5

Collinear input
The first three atoms of an input structure must not be collinear. This avoids a known bug in the
old MOPAC code. Reorder the atoms in the input file to avoid this problem.

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MOPAC Guide

Getting Help

Schrdinger software is distributed with documentation in PDF format. If the documentation is

not installed in $SCHRODINGER/docs on a computer that you have access to, you should install
it or ask your system administrator to install it.
For help installing and setting up licenses for Schrdinger software and installing documentation, see the Installation Guide. For information on running jobs, see the Job Control Guide.
The manuals are also available in PDF format from the Schrdinger Support Center. Local
copies of the FAQs and Known Issues pages can be viewed by opening the file
Suite_2009_Index.html, which is in the docs directory of the software installation, and
following the links to the relevant index pages.
If you have questions that are not answered from any of the above sources, contact Schrdinger
using the information below.
E-mail:
USPS:
Phone:
Fax:
WWW:
FTP:

help@schrodinger.com
Schrdinger, 101 SW Main Street, Suite 1300, Portland, OR 97204
(503) 299-1150
(503) 299-4532
http://www.schrodinger.com
ftp://ftp.schrodinger.com

Generally, e-mail correspondence is best because you can send machine output, if necessary.
When sending e-mail messages, please include the following information:

All relevant user input and machine output

MOPAC purchaser (company, research institution, or individual)
Primary MOPAC user
Computer platform type
Operating system with version number
Version numbers of products installed for MOPAC
mmshare version number

On UNIX you can obtain the machine and system information listed above by entering the
following command at a shell prompt:
$SCHRODINGER/utilities/postmortem

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Getting Help

This command generates a file named username-host-schrodinger.tar.gz, which you

should send to help@schrodinger.com. If you have a job that failed, enter the following
command:
$SCHRODINGER/utilities/postmortem jobid
where jobid is the job ID of the failed job, which you can find in the Monitor panel. This
command archives job information as well as the machine and system information, and
includes input and output files (but not structure files). If you have sensitive data in the job
launch directory, you should move those files to another location first. The archive is named
jobid-archive.tar.gz, and should be sent to help@schrodinger.com instead.
If Maestro fails, an error report that contains the relevant information is written to the current
working directory. The report is named maestro_error.txt, and should be sent to
help@schrodinger.com. A message giving the location of this file is written to the terminal
window.
More information on the postmortem command can be found in Appendix A of the Job
Control Guide.
On Windows, machine and system information is stored on your desktop in the file
schrodinger_machid.txt.On Windows XP and Windows 2000, is not set by default, but
should correspond to %USERPROFILE%\Local Settings\Application Data.

14

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