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A Quick Guide to MOPAC

MOPAC is a semi-empirical quantum mechanics (SQM) package,


it has become the QM package of choice in biological calculations.
SQM speeds up quantum mechanics calculations by substituting
many intermediate calculations with their empirically determined
values. As such, it relies on specific parameter sets. MOPAC parameter sets are mostly oriented to biochemistry.
MOPAC PARAMETER SETS
Default. Latest and most accurate. Reported to have problems with G-C planarity in nucleic acids.
PM7-TS
PM7 version to use in transition state reaction
calculations to obtain more accurate barrier heights.
PM6
Good H-bonds, but low accuracy for dipoles and zwitterions. Superseded by PM7.
PM6-D3
Add correction for dispersion/correlation.
PM6-DH2
Add correction for dispersion and H-bonds.
PM6-DH+
Also add correction for calculating interaction
and binding energies.
PM6-DH2X
DH2 with corrections for halogen-O and halogen-N interactions.
RM1
AM1 re-parametrized for H, C,N, O, P, S, F, Cl, Br and I.
AM1
Used for lanthanides and sparkles.
Generally it is better to use the latest parameter sets (currently
PM7 or PM7-TS for the calculation of transition states). The PM6Dx variants are good for computing intermolecular interactions.
Optionally RM1 may be useful for faster calculation of heats of
formation (HoF) and geometry optimisation.
PM7

MOPAC INPUT FILE


Keywords to control the calculation are stated in the first line. If
more lines are needed they can be added by including keyword '+'.
If the line is empty, the default is to make an optimisation calculation using the most modern parameter set. Detailed information on
the parameters can be found at
http://openmopac.net/manual/allkeys.html
Two free format lines follow and are ignored. You can use them to
describe the system.
Atoms and coordinates follow next: they can be in either internal
or cartesian MOPAC coordinate format or in PDB format.
Cartesian coordinate format contains one line per atom consisting
of the atom name, and each of its three X, Y and Z coordinates followed by a -1, 0 or 1 to indicate whether that coordinate should be

fixed (0), optimised (1) or considered a reaction coordinate (-1).


(repeat ID for chain fragments).
Coordinates end with a blank line.
XENO=(Cnn=R,..)
Specify residue names (chain ID
number = name): e.g., XENO=(A1=MSE,B1=ATP).
Any additional data needed follows after the blank line (e.g. a
second coordinate set in a SADDLE or TS calculation, atoms to START_RES=(nC,..) Specify start residue numbers n for
bind with SETPI, etc..).
incomplete chains C: e.g., START_RES=(13A).
CVB=(n1:[+-]n2)
Add or remove bonds between atoms
You may concatenate several input files.
n1
and
n2:
e.g.,
CVB=(15:-3).
Next is an example input file for H2+ optimisation:
SETPI
Information on additional bonds follows after the coPM7 OPT BONDS AUX GRAPHF GNORM=0.01 +
ordinates.
CHARGE=+1
H2+
SITE=(Cnn([+-0]),..)
Define ionization state for
Optimize geometry and save extra info
specific residues: e.g., SITE=(A123(+),B1(++)).
H
0.0
1
0.0
1
0.0
1
IONIZE Used with ADD-H forces the ionisation of all ionisable
H
1.0
1
0.0
1
0.0
1
residues in a protein.
FREQUENTLY USED KEYWORDS
METAL=(a,b...)
Treat the atoms listed as 100% ionic.
SETUP="file" Read extra keywords from an external file.
GEO-OK Accept the input geometry as is (i.e. do not check it).
0SCF
Read data and do nothing (used to check input correct- GEO-REF="FILENAME" Use geometry in FILENAME as a
ness or in combination with RESEQ).
reference during optimisation. "SELF" is a special
case. The reference must be in MOPAC format.
1SCF
Do a single point SCF calculation and stop (to compute
ground state properties).
ADD-H
Add all hydrogen atoms to a protein structure (should
be optimised afterwards).
OPT
Optimise the geometry.
OPT-H
Optimise positions of hydrogen atoms (used with
OPT-X Optimise only atoms of type 'X'.
NOOPT to avoid also optimising all other atoms).
FORCE Compute vibrational frequencies.
GNORM=n.nn
Stop optimisation when the gradient norm
ESP
Compute spin density (e.g. for display in GABEDIT).
drops below n.nn.
MULLIK Compute Mulliken's population analysis (useful to asMMOK
Allow Molecular Mechanics correction for peptide
sign atomic charges).
-CO-NH- bonds in protein calculations.
THERMO Calculate thermodynamic values (entropy, heat capaEPS=
n.nn
Value of the dielectric constant in COSMO
city, internal energy, etc..).
implicit solvent calculations (default EPS=78.4).
UHF
Carry out an Unrestricted Hartree-Fock calculation; deRSOLV=n.nn
Radius of the solvent in COSMO calculations
fault for radicals (systems with odd number of e-).
(default RSOLV=1.3).
AUX
Output an auxiliary file with additional information (e.g.
RESIDUES
In the output, save information for each atom
for use with GABEDIT).
indicating which residue it belongs to.
BONDS Print final bond matrix (useful to examine bond order).
PDBOUT Produce an output file with the coordinates in PDB
GRAPH Generate a file with graphical information (e.g. for use
format. Coordinates may be unsorted.
in MOLDEN).
RESEQ
Re-sequence (sort) all atoms by their residue as expecGRAPHF Generate a formatted file with graphics information (e.g.
ted by PDB.
for JMOL or MOPETE).
pKa
Print pKa for ionisable H attached to O atoms.
GRADIENTS
Compute and print all gradients (useful for tension and Molecular Dynamics calculations).
KEYWORDS USEFUL FOR SPECIAL SIMULATIONS
KEYWORDS USEFUL FOR PROTEIN CALCULATIONS
THREADS=n
Limit to n the threads used in a parallel run.
MOZYME Use localised orbitals to speed up calculations.
SHUT
To stop a long calculation, create a non empty file
with the same name and terminated in ".end".
PDB
Input coordinates are in PDB format.
RESTART Restart a previously stopped calculation.
CHARGES Calculate the total charge of the system.
CHAINS=(abc..)
Specify order of chains in a PDB file EXCITED Compute first excited state of the molecule.

P=n.nn Apply a pressure of n.nn Newton/m3.


T=n[H/D/W/M] Set maximum running time to "n"
seconds/Hours/Days/Weeks/Months.
OLDGEO Use last computed geometry (on multiple-job files)

GNORM=20 GEO_REF="SELF".

KEYWORDS USEFUL FOR REACTION MODELS

Run final 1SCF RESIDUES and RESEQ calculations to check that


all, especially the active site and any hetero group(s), is OK.

Optimise reactants and products to find intermediate


transition state.
TS
Optimise transition state (used after a SADDLE calculation).
FORCETS Run a FORCE calculation on a TS to check that it is at
an inflection point (reactive atom(s) have an imaginary, "negative" vibration).
IRC
Calculate intrinsic reaction coordinate (compute trajectory from TS to reactants/products).
DRC
Dynamic reaction coordinate calculation.
KINETIC=n.nn Additional kinetic energy (n.nn kcal/mol) for
a DRC calculation.
VELOCITY
Initial velocity vector for a DRC calculation.
POINT=n Number of points to use in a reaction path calculation.
SADDLE

WORKING WITH PROTEINS


Start from a PDB file. Inspect it: if it does not contain the full
chain, use START_RES to specify initial amino acids. If chains are
not in consecutive alphabetic order, or if a chain is discontinuous,
use CHAINS to specify them. If there are non-protein molecules or
modified amino acids, specify them with XENO.

Iteratively optimise the structure: run an intial calculation with


OPT GNORM=10 CUTOFF=6 T=4W, after it is finished, perform
an additional refinement with OPT GNORM=5 CUTOFF=9 T=4W.

LOCATING TRANSITION STATES


Know your system in detail. Read all available bibliography.
Prepare datasets representing reactants and products. Spend as
much time as needed getting the initial configurations right.
Using GEO_REF="<products>.MOP", move the reactants towards the products and vice versa. Repeat if needed.
When both structures are close, run a SADDLE calculation.
Refine the transition state with TS, and verify the result with a
FORCETS calculation. Repeat if needed.
From a transition state, run IRC or DRC calculations towards the
reactants and products to model the full reaction path.
MOPAC SITE, DOWNLOADS AND MANUAL
http://openmopac.net/
NOTICE: This guide only contains MOPAC key words frequently used in
biochemical calculations. Some key words may not be available in older
versions of MOPAC. Visit MOPAC web site to consult the manual for detailed information, examples and tutorials.

COPYRIGHTS
Use MOPAC to add all hydrogens: copy the PDB file to a .MOP
file and run MOPAC. If you need to use additional keywords, add MOPAC: is a trade mark of and by James J. P. Stewart
three lines before the PDB file and use the first line to enter your <MrMOPAC@OpenMOPAC.net>.
keywords and ADD-H.
CITATION: MOPAC2012, James J. P. Stewart, Stewart Computational
Run a calculation with keywords CHARGES RESIDUES. Verify Chemistry, Colorado Springs, CO, USA, http://OpenMOPAC.net/ (2012).
that all residues have the expected number of hydrogen atoms.
THIS DOCUMENT: was written and designed by Jos R. Valverde from
the Spanish EMBnet node (CNB/CSIC) and is being distributed by

Run an intial optimisation on the H atoms only using NOOPT EMBnet's P&PR Committee.
OPT-H GNORM=20.

EMBnet the Global Bioinformatics Network is a world-wide support net-

Check the ionisation states: look for ANION and CATION entries. work. Many countries have national or local nodes providing training
Verify salt bonds and that, for every ion, there is a counterion courses and other forms of help for users of bioinformatics software.
nearby. Check potential H-bonds. Ionise "by hand" any needed Find more information about your nearest node from EMBnet's web site:
groups (e.g., phosphates) using SITE. Correct bond orders using
SETPI, and eliminate spurious bonds with CVB.
http://www.embnet.org/
It may be helpful to run a 1SCF calculation to compute properties
and a RESEQ calculation to reorder atoms as expected by PDB.

A Quick Guide To MOPAC


First edition 2014
LICENSE: CC-BY-NC 3.0 http://creativecommons.org/licenses/by-nc/
Apply a chemical correction to the original X-ray or NMR structure, running an optimisation using itself as a reference with OPT THANKS to James J. P. Stewart, Domenica D'Elia and Terri Attwood.

MOPAC