Subject: Re: CCL:charmm parameter

From: "Dr. Richard L. Wood" <[email-masked]>
Date: Thu, 29 Nov 2001 09:20:26 -0500

Hi all

I apologize for the length of this in advance.  But this is info for those that have asked about
where to find parameters for CHARMM force fields.  It is taken from http://master2.lobos.nih.gov/Charmm/c28a2/parmfile.html.

I hope this helps and again I apologize for its length.

Richard

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File: Parmfile -=- Node: PARMDATA
Up: Top -=- Previous: Conversion -=- Next: Top

(A) Topology files
    (1)  top_all22_prot.inp       all hydrogen RTF for proteins
    (2)  top_all22_model.inp      all hydrogen RTF for protein model cmpds
    (3)  top_all22_sugar.rtf      all hydrogen RTF for sugars
    (4)  top_all27_na.rtf         all hydrogen RTF for nucleic acids
    (5)  top_all27_lipid.rtf      all hydrogen RTF for lipids
    (6)  top_all27_na_lipid.rtf   all hydrogen RTF for nucleic acids and lipids
    (7)  top_all27_prot_na.rtf    all hydrogen RTF for proteins and nucleic acids
    (9)  top_all27_prot_lipid.rtf all hydrogen RTF for proteins and lipids
    (9)  toph19.inp               extended atom RTF for proteins
    (10) toprna10r_22.inp         extended atom RTF for nucleic acids

(B) Parameter files
    (1)  par_all22_prot.inp       all hydrogen parameters for proteins
    (2)  par_all22_sugar.rtf      all hydrogen parameters for sugars
    (3)  par_all27_na.rtf         all hydrogen parameters for nucleic acids
    (4)  par_all27_lipid.rtf      all hydrogen parameters for lipids
    (5)  par_all27_na_lipid.rtf   all hydrogen parameters for nucleic acids and lipids
    (6)  par_all27_prot_na.rtf    all hydrogen parameters for proteins and nucleic acids
    (7)  par_all27_prot_lipid.rtf all hydrogen parameters for proteins and lipids
    (8)  param19.inp              extended atom parameters for proteins
    (9)  pardna10_22.inp          extended atom parameters for nucleic acids
    (10) par_hbond.inp            hydrogen bond parameters for analysis only

Phased out: The CHARMM22 all-atom nucleic acid and lipid topology and
parameter files are no longer included in the toppar directory due to
their becoming obsolete.  Note that they are included in the
toppar_history directories.

The CHARMM all-hydrogen topology and parameter sets may be
considered to be stable, however, minor bug fixes may be performed as
required.  Additions may also occur leading to an expanding set of
parameters which are compatible across proteins, nucleic acids,
lipids, and, ultimately, carbohydrates.  The carbohydrate(sugar)
parameter work is still in progress by John Brady and coworkers; the
number of sugar types should expand in the future.  See the file
toppar_all.history for a listing changes in the files over time.
top_all22_model.inp includes the majority of model compounds used in
the protein parameterization and is to be used in conjunction with
par_all22_prot.inp.

Three sets of combined topology and parameter files are included
for use with 1) proteins and nucleic acids, 2) protein and lipids
and 3) nucleic acids and lipids.  In all cases the CHARMM22 protein
parameters and the CHARMM27 nucleic acid or lipid parameters are
used.  The designation all27 for these files is based on the
use of the most recent nucleic acid or lipid parameters.  Test
calculations using these combined files have yielded good results.

Added as of July 1997 was the parameter file par_hbond.inp.  This file
is included for the analysis of hydrogen bonds; it includes
information to calculate h-bond energies, but these are basically
meaningless.  The hydrogen bonds should NOT be used for energy,
minimization and dynamics calculations with the CHARMM all-hydrogen
topology and parameter sets.

Ions in the all22 files are from two sources.  Mg and Ca are from
Prodhom and Karplus and were optimized specifically for the all22
parameters.  The remaining cations are from Benoit Roux (see his
thesis).  They were optimized to be consistent with Param19, however,
MD studies in a number of groups have shown them to work well.  Note
the presence of a variety of NBFIXES for the ions.  These were
initially optimized based on the proteins and later transferred to the
lipids and nucleic acids based on analogy (by ADM Jr.).  Ions in the
all27 files have been optimized based on free energies of solvation
by Roux and coworkers.  As of August 1999 there were no NBFIXes
used with these ions.

The extended atom parameters for proteins are the same as those
included with CHARMM20 which are based on Wally Reiher's thesis.  They
have been included in the supplement material of a recent publication
(see suggested citations below).  For the extended atom nucleic acid
parameters those of Nilsson and Karplus, J. Comp.  Chem.  7:591-616,
1986 are used which were also included in the CHARMM20 release and are
the only set to include explicit hydrogen bonding terms.  Some
alterations of the extended atom nucleic acid topology and parameter
files have been made in order to maintain compatibility with the
multiple dihedral scheme in CHARMM22.

Please send all remarks and suggestions to [email-masked].

ADM Jr., August 1999
http://www.pharmacy.ab.umd.edu/~alex/

References

PARAM19 PROTEIN PARAMETERS

Reiher, III., W.E. Theoretical Studies of Hydrogen Bonding, Ph.D.
Thesis, Department of Chemistry, Harvard University, Cambridge, MA,
USA, 1985

and

Neria, E., Fischer, S., and Karplus, M.  Simulation of Activation Free
Energies in Molecular Systems, Journal of Chemical Physics, 1996, 105:
1902-21.

EXTENDED ATOM NUCLEIC ACID PARAMETERS

Nilsson, L. and Karplus,M. Empirical Energy Functions for Energy
Minimizations and Dynamics of Nucleic Acids J. Comp.  Chem.
7:591-616, 1986

CHARMM22 PROTEIN PARAMETERS

MacKerell, J., A.D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R. L.;
Evanseck, J.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.;
Joseph, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.;
Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, I., W. E.;
Roux, B.; Schlenkrich, M.; Smith, J.; Stote, R.; Straub, J.; Watanabe,
M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M.  All-hydrogen
Empirical Potential for Molecular Modeling and Dynamics Studies of
Proteins using the CHARMM22 Force Field.  Journal of Physical
Chemistry B, 1998, 102, 3586-3616.

FOR PHOSPHOTYROSINE

Feng, M.-H., Philippopoulos, M., MacKerell, Jr., A.D., and Lim, C.
Structural Characterization of the Phosphotyrosine Binding Region of a
High-Affinity SH2 Domain-Phosphopeptide Complex by Molecular Dynamics
Simulation and Chemical Shift Calculations, Journal of the American
Chemical Society, 1996, 118: 11265-11277

CHARMM27 NUCLEIC ACID PARAMETERS

Foloppe, N. and MacKerell, Jr., A.D. "All-Atom Empirical Force Field for
Nucleic Acids: 2) Parameter Optimization Based on Small Molecule and
Condensed Phase Macromolecular Target Data.  Journal of Computational
Chemsitry, 2000, 21:86-104.

and

MacKerell, Jr., A.D. and Banavali, N. "All-Atom Empirical Force Field for
Nucleic Acids: 2) Application to Molecular Dynamics Simulations of DNA
and RNA in Solution.  Journal of Computational Chemsitry, 2000, 21:105-120.

CHARMM27 LIPID PARAMETERS

Feller, S. and MacKerell, Jr., A.D. manuscript in preparation.

NAD+, NADH and PPI

Pavelites, J.J., Bash, P.A., Gao, J. and MacKerell, Jr., A.D. A
Molecular Mechanics Force Field for NAD+, NADH, and the Pyrophosphate
Groups of Nucleotides, Journal of Computational Chemistry, 1997, 18:
221-239.

CHARMM22 NUCLEIC ACID PARAMETERS

MacKerell Jr., A.D., Wiorkiewicz-Kuczera, J. and Karplus, M. An
all-atom empirical energy function for the simulation of nucleic
acids, Journal of the American Chemical Society, 1995,
117:11946-11975.

CHARMM22 LIPID PARAMETERS

Schlenkrich, M., Brickmann, J., MacKerell, Jr., A.D., and Karplus, M.
Empirical Potential Energy Function for Phospholipids: Criteria for
Parameter Optimization and Applications, in "Biological Membranes: A
Molecular Perspective from Computation and Experiment," K.M. Merz and
B. Roux, Eds. Birkhauser, Boston, 1996, pp 31-81.

FOR ALKENES

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

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--
Richard L. Wood, Ph. D.
Physical/Computational Chemist
Post-doctoral Associate
Department of Food Science
120 Stocking Hall
Cornell University, Ithaca, NY 14853