pcGAMESS QM/MM INPUT DOCUMENTATION

PC GAMESS QM/MM INPUT DOCUMENTATION

(01Aug07 revision)

NOTE: This is version 6.4 of PC GAMESS.

The presence of the $MOLMEC namelist in the pcGAMESS input data stream triggers the QM/MM functionality.

QM/MM Functionality is supported for the following:

· Runtyp=OPTIMIZE, ENERGY, GRADIENT, HESSIAN (numerical)

· DFT

· SCF=RHF, UHF

· MPLEVEL=0, 2

· COORD=UNIQUE

· PTGRP=C1

· Internal or general basis sets

· Maximum of 3500 Q+C+M total atoms (see below for definitions)

Note: QM/MM functionality will only work for COORD=UNIQUE and symmetry point group C1

QM/MM functionality is provided using an integrated version of the Tinker Molecular Mechanics Package (v3.7) developed by Professor Jay William Ponder of the Washington University School of Medicine. UFF functionality was independently integrated by Jim Kress.

This integration implements version 3.7 of the Tinker Molecular Mechanics (MM) program. NO OTHER VERSION OF TINKER IS SUPPORTED. Tinker is regularly updated by Professor Ponder and his group. New versions of Tinker are not guaranteed (by Professor Ponder, et al) to provide backwards compatibility with older version input (xyz) or parameter (prm) files. Also, we do not guarantee that the MM capabilities integrated into pcGAMESS will be kept current with the Tinker programs as they evolve.

In addition, only the MM parameter files distributed with pcGAMESS will provide proper results. The use of ANY OTHER MM parameter files will not yield correct answers.

As of 17Feb08, the QM/MM version of PCGAMESS will support a maximum of 3500 atoms (=Q+C+M)

$MOLMEC group

This group of parameters provides control over the QM/MM functionality in pcGAMESS. It is required for QM/MM calculations.

TYPE = Is the name of the desired MM Force Field, e.g. UFF, MM3, etc. The default value is TYPE=UFF. The MM parameter filename is taken as TYPE.prm, e.g. for TYPE=UFF the MM parameter file name should be uff.prm. Similarly, for TYPE=MM3, the filename should be MM3.prm.

Note: when running in parallel, the force field parameter file must be located ini the same directory with the pcgamess executable on all nodes being used

Special note for type=UFF

Atom types 126 and 127 have been altered to allow the inclusion of TIP3 water molecules as UFF MM molecules in QM calculations. Type 126 is HTIP3 and Type 127 is OTIP3.

RDCAP = A logical variable that specifies if the initial cap atom coordinates will be read from the pcGAMESS input file. The default value is .false. The cap coordinates will be in Angstroms. If any cap atoms coordinates are to be read, input for ALL capping atoms must be provided.

This capability is essential if one wants to restart a previous calculation (e.g. an optimization that did not finish) or wants to use the results of a prior QM/MM calculation in a new calculation (e.g. take results from an optimization and calculate the hessian and normal modes).

Within the pcGAMESS input file, the cap geometry information is contained within the $CAPINP group. The cap coordinate data follows a $CAPINP line, one line per cap atom each following the regular GAMESS input format. I.e. name, charge, x, y, z. The name and charge will be ignored but are included for the user's convenience. The cap coordinate data is followed by a line containing $END

MMPRT = A logical variable that specifies if MM type information for each atom (Q,C and M) will be printed with all coordinate and gradient output. If = .false. then the normal GAMESS output will be generated. The default value is .false.

This was done to allow QM/MM calculations to generate GAMESS output that will not break the myriad GAMESS parsers out there, e.g. MOLEKEL, gOpenMol, etc. Note: in either case, cap atom info will be printed in the GAMESS output file so geometries parsed from the GAMESS file will include Cap atoms.

CHGKEY = A logical variable that specifies if the atom charges used for MM force fields will be read from the pcGAMESS input file using the $CHGINP group. The default value is .false.

Within the pcGAMESS input file, the atom charge information is contained within the $CHGINP group. The atom charge data follows a $CHGINP line, one line per atom each

containing the atom number and charge following the regular GAMESS input format. The charge data is followed by a line containing $END. No blank lines are allowed.

Note: these charges are relevant for both QM and MM atoms. Charge information for the MM representation of the QM atoms can be set, too.

PRTCHG = A logical variable that (when .true.) results in MM charges on all atoms being printed at the beginning of the calculation at the initial geometry. The default value is .false. In the case of UFF, Qeq charges are printed at each new geometry throughout the calculation.

QPOL = THIS IS NOT IMPLEMENTED IN THE CURRENT VERSION.

A logical variable that (when .true.) results in QC atoms being polarized by MM charges. If .false. no polarization occurs. The default value for QPOL is false. QPOL can only be used with the UFF force field with QEQ charges enabled (TYPE=UFF USEQEQ=.true.) or the AMBER force field.

For TYPE=UFF, the following options apply:

READBO = A logical variable that specifies if additional bond order information will be read from the pcGAMESS input file. It is only used if TYPE=UFF. The default value is.false.

For UFF bond order specification is required for all bonds. The program sets all bond orders = 1 for all bonds specified in the input file. If any bonds are not single bonds, the user MUST specify their bond order using READBO.

For READBO=.true., the bond order information follows a $BNDORD line, one line per each bond order specification. Each bond order is specified as i j bond_order where i and j are atom numbers and bond_order is the order of the bond between atoms i and j. The bond order data is followed by a line containing $END

USEQEQ = A logical variable that specifies if QEQ charges are generated. If false, the usual covalent UFF is used. The default value for USEQEQ is false. QEQ charges can only be used with the UFF force field.

QM/MM functionality requires $DATA geometry specification data be modified as follows:

Geometry is specified as:

Atm_Name Nuc_Chrge X_Coord Y_Coord Z_Coord MM_Type Atom_Type MM_Atom_Conct

1) Atm_Name, Nuc_Chrge, X_Coord, Y_Coord, and Z_Coord have their usual pcGAMESS definitions.

2) MM_Type takes one of three Character values, Q, M, or C.

a)A Q designation indicates pcGAMESS should treat this atom as a regular QM atom

b)A M designation indicates pcGAMESS should treat this atom as a MM atom

c)A C designation indicates pcGAMESS should treat this atom as a 'capping' atom.

3) Atom_Type is the appropriate MM atom type as specified in the TYPE.prm file used in the

pcGAMESS/MM calculation.

4) MM_Atom_Conct is a space delimited, integer list of atoms that are directly connected

to Atom_Name being specified

5) All atoms to be capped must be explicitly specified. That is done by marking the

interface atoms as having a negative entry in the input connectivity line for the

interface atom. For example:

C1 6 0.96893124 1.31494824 0.00993246 C 8 -2 5 9 10

In this example, C1 serves as the interface atom between the QM and MM regions.

It's connection to QC atom 2 will be assigned one capping hydrogen atom using

the appropriate covalent radii for the initial specification of the coordinates

for the capping hydrogen.

6) If using general basis input, each cap atom must have a separate basis set specified.

For example, if a cap atom is specified as:

Si16 14.0 1.95469 -1.26061 0.01872 C 11 -1 -3 37 38

Then each capping atom (-1 and -3) must have it's capping atom hydrogen basis

specified. The input would look like this:

Si16 14.0 1.95469 -1.26061 0.01872 C 11 -1 -3 37 38

S 2

1 4.501800 0.156285

2 0.681444 0.904691

S 1

1 0.151398 1.000000

S 2

1 4.501800 0.156285

2 0.681444 0.904691

S 1

1 0.151398 1.000000

During the input process, a hydrogen atom will be automatically spawned for each

capping atom. The spawned H atom will be given a label composed of the input

label for the capping atom followed by a _C

Also as a part of the input process, a MM atom will be spawned for each capping atom.

The spawned MM atom will be given a label composed of the input label for the capping

atom followed by a _B.

An example: Atom C12 is designated as a capping atom. During the input

process, a hydrogen atom labelled C12_C will be added to the QC atom list

and a MM atom labelled C12_B will be placed in the total atom list. Thus,

the capping atom C12 yields 2 elements in the atom list used in the

calculation. One is C12_C (the spawned hydrogen atom) and the other is

C12_B, a MM atom.

7) In $DATA, no blank cards are required after M atoms

Examples of QM/MM input can be found at the end of this file and in the directory named QMMM sample files

As of 17Feb08, the QM/MM version of PCGAMESS will support a maximum of 3500 atoms (=Q+C+M)

---------------------------------------------------------------------

FORCE FIELD PARAMETER SETS

This section is taken from the Tinker v3.7 User Guide. Force Field parameter files will be found in the directory named MM_prm_files. Note: on Linux systems, the force field parameter file names must be all upper case, e.g. UFF.PRM

The TINKER package is distributed with several force field parameter sets, implementing a selection of widely-used literature force fields as well as the TINKER force field currently under construction in the Ponder lab. We try to exactly reproduce the intent of the original authors of our distributed, third-party force fields. In all cases the parameter sets have been validated against literature reports, results provided by the original developers, or calculations made with the authentic programs. With the few exceptions noted below, TINKER calculations can be treated as authentic results from the genuine force fields. A brief description of each parameter set, including some still in preparation and not distributed with the current version, is provided below with lead references:

AMBER.PRM

AMBER-95 parameters for proteins. The nucleic acid parameters are not implemented yet. Note that with their ‘‘Cornell’’ force field, the Kollman group has devised separate, fully independent partial charge values for each of the N- and C-terminal residues. At present, the terminal residue charges for TINKER’s version maintain the correct formal charge, but redistributed somewhat from the Kollman group values. The file reproduces the authentic parm94 set; torsional parameter changes for parm96 are noted in that section of the file.

W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, Jr., D. M. Ferguson, D. C. Spellmeyer, T.

Fox, J. W. Caldwell and P. A. Kollman, A Second Generation Force Field for the Simulation of Proteins,

Nucleic Acids, and Organic Molecules", J. Am. Chem. Soc., 117, 5179-5197 (1995) [PARM94]

P. Kollman, R. Dixon, W. Cornell, T. Fox, C. Chipot and A. Pohorille, The Development/ Application of a ’Minimalist’ Organic/Biochemical Molecular Mechanic Force Field using a Combination of ab Initio Calculations and Experimental Data, in Computer Simulation of Biomolecular Systems, W. F. van Gunsteren, P. K. Weiner, A. J. Wilkinson, eds., Volume 3, 83-96 (1997) [PARM96]

G. Moyna, H. J. Williams, R. J. Nachman and A. I. Scott, Conformation in Solution and Dynamics of a Structurally Constrained Linear Insect Kinin Pentapeptide Analogue, Biopolymers, 49, 403-413 (1999) [AIB charges]

W. S. Ross and C. C. Hardin, Ion-Induced Stabilization of the G-DNA Quadruplex: Free Energy Perturbation Studies, J. Am. Chem. Soc., 116, 4363-4366 (1994) [Alkali Metal Ions]

J. Aqvist, Ion-Water Interaction Potentials Derived from Free Energy Perturbation Simulations, J. Phys. Chem., 94, 8021-8024, 1990 [Alkaline Earth Ions, radii adapted for AMBER combining rule]

CHARMM.PRM

CHARMM22 parameters for proteins. Most of the nucleic acid, lipid and small model compound parameters are not yet implemented.

A. D. MacKerell, Jr., J. Wiorkeiwicz-Kuczera and M. Karplus, An All-Atom Empirical Energy Function for the Simulation of Nucleic Acids, J. Am. Chem. Soc., 117, 11946-11975 (1995)

A. D. MacKerrell, Jr., et al., All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins, J. Phys. Chem. B, 102, 3586-3616 (1998)

S. E. Feller, D. Yin, R. W. Pastor and A. D. MacKerell, Jr., Molecular Dynamics Simulation of Unsaturated Lipids at Low Hydration: Parametrization and Comparison with Diffraction Studies, Biophysical Journal, 73, 2269-2279 (1997) [alkenes]

R. H. Stote and M. Karplus, Zinc Binding in Proteins and Solution - A Simple but Accurate

Nonbonded Representation, Proteins, 23, 12-31 (1995) [zinc ion]

MM2.PRM

Full MM2(91) parameters including pi-systems. The anomeric and electronegativity correction terms are not implemented.

N. L. Allinger, "Conformational Analysis. 130. MM2. A Hydrocarbon Force Field Utilizing V1 and V2 Torsional Terms", J. Am. Chem. Soc., 99, 8127-8134 (1977)

J. T. Sprague, J. C. Tai, Y. Yuh and N. L. Allinger, The MMP2 Calculational Method, J. Comput. Chem., 8, 581-603 (1987)

N. L. Allinger, R. A. Kok and M. R. Imam, Hydrogen Bonding in MM2, J. Comput. Chem., 9, 591-595 (1988)

All parameters distributed with TINKER are from the "MM2 (1991) Parameter Set", as provided by N. L. Allinger, University of Georgia

MM3.PRM

Full MM3(99) parameters including pi-systems. The directional hydrogen bonding term is implemented, but the anomeric, electronegativity, Bohlmann correction terms are not implemented.

N. L. Allinger, Y. H. Yuh and J.-H. Lii, Molecular Mechanics. The MM3 Force Field for Hydrocarbons. 1, J. Am. Chem. Soc., 111, 8551-8566 (1989)

J.-H. Lii and N. L. Allinger, Molecular Mechanics. The MM3 Force Field for Hydrocarbons. 2. Vibrational Frequencies and Thermodynamics, J. Am. Chem. Soc., 111, 8566-8575 (1989)

J.-H. Lii and N. L. Allinger, Molecular Mechanics. The MM3 Force Field for Hydrocarbons. 3. The van der Waals’ Potentials and Crystal Data for Aliphatic and Aromatic Hydrocarbons, J. Am. Chem. Soc., 111, 8576-8582 (1989)

N. L. Allinger, H. J. Geise, W. Pyckhout, L. A. Paquette and J. C. Gallucci, Structures of Norbornane and Dodecahedrane by Molecular Mechanics Calculations (MM3), X-ray Crystallography, and Electron Diffraction, J. Am. Chem. Soc., 111, 1106-1114 (1989) [torsion-stretch]

N. L. Allinger, F. Li and L. Yan, Molecular Mechanics. The MM3 Force Field for Alkenes, J. Comput. Chem., 11, 848-867 (1990)

N. L. Allinger, F. Li, L. Yan and J. C. Tai, Molecular Mechanics (MM3) Calculations on Conjugated Hydrocarbons, J. Comput. Chem., 11, 868-895 (1990)

J.-H. Lii and N. L. Allinger, Directional Hydrogen Bonding in the MM3 Force Field. I, J. Phys. Org. Chem., 7, 591-609 (1994)

J.-H. Lii and N. L. Allinger, Directional Hydrogen Bonding in the MM3 Force Field. II, J. Comput. Chem., 19, 1001-1016 (1998)

All parameters distributed with TINKER were translated from "MM3 PARAMETERS (1999)" as updated on January 17, 1999 and obtained from the above web sites

MM3PRO.PRM

Protein-only version of the MM3 parameters.

J.-H. Lii and N. L. Allinger, The MM3 Force Field for Amides, Polypeptides and Proteins, J. Comput. Chem., 12, 186-199 (1991)

OPLS.PRM

Complete OPLS-UA with united-atom parameters for proteins and many classes of organic molecules. Explicit hydrogens on polar atoms and aromatic carbons.

W. L. Jorgensen and J. Tirado-Rives, The OPLS Potential Functions for Proteins. Energy Minimizations for Crystals of Cyclic Peptides and Crambin, J. Am. Chem. Soc., 110, 1657-1666 (1988) [Protein & Peptide]

W. L. Jorgensen and D. L. Severance, Aromatic-Aromatic Interactions: Free Energy Profiles for the Benzene Dimer in Water, Chloroform, and Liquid Benzene, J. Am. Chem. Soc., 112,4768-4774 (1990) [Aromatic Hydrogens]

S. J. Weiner, P. A. Kollman, D. A. Case, U. C. Singh, C. Ghio, G. Alagona, S. Profeta, Jr. and P. Weiner, A New Force Field for Molecular Mechanical Simulation of Nucleic Acids and Proteins, J. Am. Chem. Soc., 106, 765-784 (1984) [United-Atom "AMBER/OPLS" Local Geometry]

S. J. Weiner, P. A. Kollman, D. T. Nguyen and D. A. Case, An All Atom Force Field for Simulations of Proteins and Nucleic Acids, J. Comput. Chem., 7, 230-252 (1986) [All-Atom "AMBER/OPLS" Local Geometry]

L. X. Dang and B. M. Pettitt, Simple Intramolecular Model Potentials for Water, J. Phys. Chem., 91, 3349-3354 (1987) [Flexible TIP3P and SPC Water]

W. L. Jorgensen, J. D. Madura and C. J. Swenson, Optimized Intermolecular Potential Functions for Liquid Hydrocarbons, J. Am. Chem. Soc., 106, 6638-6646 (1984) [Hydrocarbons]

W. L. Jorgensen, E. R. Laird, T. B. Nguyen and J. Tirado-Rives, Monte Carlo Simulations of Pure Liquid Substituted Benzenes with OPLS Potential Functions, J. Comput. Chem., 14, 206-215 (1993) [Substituted Benzenes]

E. M. Duffy, P. J. Kowalczyk and W. L. Jorgensen, Do Denaturants Interact with Aromatic Hydrocarbons in Water?, J. Am. Chem. Soc., 115, 9271-9275 (1993) [Benzene, Naphthalene, Urea, Guanidinium, TetraMeAmmonium]

W. L. Jorgensen and C. J. Swenson, Optimized Intermolecular Potential Functions for Amides and Peptides. Structure and Properties of Liquid Amides, J. Am. Chem. Soc., 106, 765-784 (1984) [Amides]

W. L. Jorgensen, J. M. Briggs and M. L. Contreras, Relative Partition Coefficients for Organic Solutes form Fluid Simulations, J. Phys. Chem., 94, 1683-1686 (1990) [Chloroform, Pyridine, Pyrazine, Pyrimidine]

J. M. Briggs, T. B. Nguyen and W. L. Jorgensen, Monte Carlo Simulations of Liquid Acetic Acid and Methyl Acetate with the OPLS Potential Functions, J. Phys. Chem., 95, 3315-3322 (1991) [Acetic Acid, Me Acetate]

H. Liu, F. Muller-Plathe and W. F. van Gunsteren, A Force Field for Liquid Dimethyl Sulfoxide and Physical Properties of Liquid Dimethyl Sulfoxide Calculated Using Molecular Dynamics Simulation, J. Am. Chem. Soc., 117, 4363-4366 (1995) [Dimethyl Sulfoxide]

J. Gao, X. Xia and T. F. George, Importance of Bimolecular Interactions in Developing Empirical Potential Functions for Liquid Ammonia, J. Phys. Chem., 97, 9241-9246 (1993) [Ammonia]

J. Aqvist, Ion-Water Interaction Potentials Derived from Free Energy Perturbation Simulations, J. Phys. Chem., 94, 8021-8024 (1990) [Metal Ions]

W. S. Ross and C. C. Hardin, Ion-Induced Stabilization of the G-DNA Quadruplex: Free Energy Perturbation Studies, J. Am. Chem. Soc., 116, 4363-4366 (1994) [Alkali Metal Ions]

J. Chandrasekhar, D. C. Spellmeyer and W. L. Jorgensen, Energy Component Analysis for Dilute Aqueous Solutions of Li+, Na+, F-, and Cl- Ions, J. Am. Chem. Soc., 106, 903-910 (1984) [Halide Ions]

Most parameters distributed with TINKER are from "OPLS and OPLS-AA Parameters for Organic Molecules, Ions, and Nucleic Acids" as provided by W. L. Jorgensen, Yale University, October 1997

OPLSAA.PRM

OPLS-AA with all-atom parameters for proteins and many general classes of organic molecules.

W. L. Jorgensen, D. S. Maxwell and J. Tirado-Rives, Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids, J. Am. Chem. Soc., 117, 11225-11236 (1996)

W. L. Jorgensen and N. A. McDonald, Development of an All-Atom Force Field for Heterocycles. Properties of Liquid Pyridine and Diazenes, THEOCHEM-J. Mol. Struct., 424, 145-155 (1998)

N. A. McDonald and W. L. Jorgensen, Development of an All-Atom Force Field for Heterocycles. Properties of Liquid Pyrrole, Furan, Diazoles, and Oxazoles, J. Phys. Chem. B, 102, 8049-8059 (1998)

All parameters distributed with TINKER are from "OPLS and OPLS-AA Parameters for Organic Molecules, Ions, and Nucleic Acids" as provided by W. L. Jorgensen, Yale University, October 1997

UFF.PRM

UFF all atom parameter set taken from the original work by Rappe’ and Goddard:

Rappe, CJ Casewit, KS Colwell, WA Goddard III, UFF - A full periodic table force field for molecular mechanics and molecular dynamics simulation, J Am Chem Soc, 1992, 114, 10024-10035

Special note for type=UFF

Atom types 126 and 127 have been altered to allow the inclusion of TIP3 water molecules as UFF MM molecules in QM calculations. Type 126 is HTIP3 and Type 127 is OTIP3.

---------------------------------------------------------------------