Re: CCL:charmm parameter



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 alex \\at// mmiris.ab.umd.edu.
 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