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Description of topology and parameter files in version c31 and
subsequent versions.
In version 31 a major restructuring of the topology and parameter
files was undertaken. This was performed to create a more modular
approach to the files, thereby avoiding the problem of files becoming
increasingly large. The restructuring was done such that the primary
topology and parameter files for biomolecules can be used as they were
previously. However, the topology and parameter information for the
majority of model compounds used in the parameter development,
additional molecules, including coenzymes, and patches parametrized to
be compatible with the CHARMM force fields have been moved to toppar
stream files. These toppar stream files have to be streamed in a
and parameter files. They include both the topology and parameter
information for the selected molecules, using the "read rtf card
append" and "read param card append" commands to append the additional
information to the topology and parameter lists. As of version c31 it
is still necessary to maintain all the MASS atom lists in the parent
topology and parameter files.
Files in Version C35/C36
Topology files
top_all22_prot.inp all hydrogen RTF for proteins, CHARMM22 with CMAP
top_all35_carb.rtf all hydrogen RTF for sugars
top_all32_lipid.rtf all hydrogen RTF for lipids with alkane dihedral update
top_all36_lipid.rtf all hydrogen RTF for lipids (C36 and on)
top_all27_na.rtf all hydrogen RTF for nucleic acids
top_all32_na_lipid.rtf all hydrogen RTF for nucleic acids and lipids
top_all36_na_lipid.rtf all hydrogen RTF for nucleic acids and lipids (C36 and on)
top_all27_prot_na.rtf all hydrogen RTF for proteins and nucleic acids
top_all32_prot_lipid.rtf all hydrogen RTF for proteins and lipids
top_all36_prot_lipid.rtf all hydrogen RTF for proteins and lipids (C36 and on)
top_all35_ethers.rtf all hydrogen RTF for ethers
top_all30_cheq_prot.inp all hydrogen RTF for protein charge equilibration polarizable model
toph19.inp extended atom RTF for proteins
toprna10r_22.inp extended atom RTF for nucleic acids
Parameter files
par_all22_prot.inp all hydrogen parameters for proteins with CMAP
par_all35_carb.prm all hydrogen parameters for sugars
par_all32_lipid.prm all hydrogen parameters for lipids with alkane dihedral update
par_all36_lipid.prm all hydrogen parameters for lipids (C36 and on)
par_all27_na.prm all hydrogen parameters for nucleic acids
par_all32_na_lipid.prm all hydrogen parameters for nucleic acids and lipids
par_all36_na_lipid.prm all hydrogen parameters for nucleic acids and lipids (C36 and on)
par_all27_prot_na.prm all hydrogen parameters for proteins and nucleic acids
par_all32_prot_lipid.prm all hydrogen parameters for proteins and lipids
par_all36_prot_lipid.prm all hydrogen parameters for proteins and lipids (C36 and on)
par_all30_cheq_prot.inp all hydrogen parameters for protein charge equilibration polarizable model
par_all35_ethers.prm all hydrogen parameters for ethers
param19.inp extended atom parameters for proteins
pardna10_22.inp extended atom parameters for nucleic acids
(C) Toppar stream files (see stream subdirectory) listed under the parent
topology and parameter files required for the individual files.
Parent files: can be used with prot, na and lipid files
toppar_dum_nobel_gases.str: dummy atom, helium and neon
toppar_hbond.str: stream file to estimate hydrogen bond interactions
Parent files: top_all22_prot.inp, par_all22_prot.inp
(or top_all22_prot_cmap.inp, par_all22_prot_cmap.inp)
toppar_all22_prot_model.str: model compounds used in protein parameter development
as well as additional compounds
toppar_all22_prot_aldehydes.str: small molecule aldehydes
toppar_all22_prot_aliphatic_c27.str: extends all22 protein force field to include
all27 alkane parameters
toppar_all22_prot_fluoro_alkanes.str: optimized fluoroalkanes, requires
toppar_all22_prot_aliphatic_c27.str
toppar_all22_prot_heme.str: heme, O2, CO, CO2 and related patches
toppar_all22_prot_pyridines.str: various substituted pyridines
toppar_all22_prot_retinol.str: retinol, model compounds, Schiff's bases
Parent files: top_all27_na.rtf, par_all27_na.prm
toppar_all27_na_model.str: model compounds used in na parameter development including
individual bases etc.
toppar_all27_na_base_modifications.str: various chemical modifications of bases
toppar_all27_na_carbocyclic.str: constrained bicyclic sugars
toppar_all27_na_nad_ppi.str: NAD, NADH, ADP, ATP and others. Useful in combination with
protein force field via the top_all27_prot_na.rtf
and par_all27_prot_na.prm
Parent files: top_all32_lipid.rtf, par_all32_lipid.prm
toppar_all27_lipid_model.str: model compounds used in lipid parameter development, including
alkenes
toppar_all27_lipid_cholesterol.str: cholesterol and related model compounds
Parent files: top_all36_lipid.rtf, par_all36_lipid.prm
toppar_all36_lipid_model.str: model compounds used in lipid parameter development, including
alkenes
toppar_all36_lipid_cholesterol.str: cholesterol and related model compounds
Parent files: top_all27_prot_na.rtf, par_all27_prot_na.prm
toppar_prot_na_all.str: all compounds that require both protein and nucleic acid toppar information
includes phosphorylated tyrosine, serine and threonine and some
coenzymes (SAH)
toppar_all27_na_bkb_modifications.str: various chemical modificaiton of the na backbone
including abasic variants and phosphoramidate
Parent files not needed
toppar_water_ions.str: contains TIP3P water model and ions. All of these
are also included in the prot, na and lipid topology
and parameter files.
toppar_amines.str: highly optimized neutral aliphatic amines.
(D) Parameters for the polarizable force field based on a classical
Drude oscillator. As this force field is currently under development
such that the parameters have been placed in the "drude" subdirectory.
Parameters for water, alkanes, ethers, aromatics, alcohols and amides
are available as of January 2007 and this list will be expanding. See
the 00readme for details and the approriate references.
(E) Parameters for selected silicate and aluminosilicate surfaces have
been developed. These parameters are designed to be compatible with
the CHARMM22 and 27 force fields allowing for biological
molecule-silicate surface interactions. As use of these parameters
requires creation of the surface, which entails creation of the
necessary patches, the parameters are included in the "silicates"
subdirectory. This directory also includes examples and code to
create the extended surfaces. See the 00readme file for more details.
ref: Lopes, P.E.M., Murashov, V. Tazi, M. Demchuk, E. MacKerell,
A. D., Jr. "Development of an Empirical Force Field for
Silica. Application to the Quartz-Water Interface," Journal of
Physical Chemistry B, 110: 2782-2792, 2006.
(F) Additional topology and parameter files from various sources are
included in subdirectories of the toppar directory. A description
follows:
non_charmm: Contains toppar files for AMBER, Bristol-Myers Squibb
(BMS) and OPLS force fields along with a stream file for the SPC and
SPC/E water models. These files have been tested to the extent that
they may be considered reliable representations of the original force
fields, though potentially not exact representations. These files are
NOT maintained and, thus, use at your own risk. See the 00readme
files and note that AMBER requires a special version of CHARMM as
described in the 00readme file.
tamdfff: An internal coordinate force field (ICFF) that was built
based on the CHARMM 22 protein force field. Specifically, it provides
a backbone covalent geometry suitable for torsion angle molecular
dynamics (TAMD) and the necessary CMAP cross-term corrections to
suppress distortions of the potential energy surface due to rigid
covalent geometry. Additional details can be found in tamd.doc.
Ref. J. Chen, W. Im and C. L. Brooks III, J. Comp. Chem. 2005, 26,
1565-1578.
rush: A simple implicit-solvent protein force-field that adds terms to
the bonded portion (bond + angle + dihe + impr + urey) of the all-atom
the hydrophobic effect (_U_nburied _S_urface), and intra-molecular and
protein-solvent hydrogen-bonding (_H_ydrogen-bonding) (hence _R_ _U_
_S_ _H_). Usage instructions are in doc/rush.doc
gbsw: Optimized protein backbone parameters (par_all22_prot_gbsw.inp)
and atomic input radii (radius_gbsw.str) for a balanced GBSW implicit
solvent force field. The backbone phi/psi cross-term (CMAP) and the
atomic input radii have been re-optimized specifically to balance the
solvation and intramolecular interactions and to capture experimental
conformational equilibria of both helical peptides and
beta-hairpins. Additional information can be found in gbsw.doc.
Ref. J. Chen, W. Im and C. L. Brooks III, J. Am. Chem. Soc. 128,
3728-36 (2006).
Description of topology and parameter files prior to version c31.
These files can be accessed via the toppar_history subdirectory of the
toppar directory.
(A) Topology files
top_all22_prot.inp all hydrogen RTF for proteins
top_all22_model.inp all hydrogen RTF for protein model cmpds
top_all22_sugar.rtf all hydrogen RTF for sugars
top_all27_na.rtf all hydrogen RTF for nucleic acids
top_all27_lipid.rtf all hydrogen RTF for lipids
top_all27_na_lipid.rtf all hydrogen RTF for nucleic acids and lipids
top_all27_prot_na.rtf all hydrogen RTF for proteins and nucleic acids
top_all27_prot_lipid.rtf all hydrogen RTF for proteins and lipids
toph19.inp extended atom RTF for proteins
toprna10r_22.inp extended atom RTF for nucleic acids
(B) Parameter files
par_all22_prot.inp all hydrogen parameters for proteins
par_all22_sugar.prm all hydrogen parameters for sugars
par_all27_na.prm all hydrogen parameters for nucleic acids
par_all27_lipid.prm all hydrogen parameters for lipids
par_all27_na_lipid.prm all hydrogen parameters for nucleic acids and lipids
par_all27_prot_na.prm all hydrogen parameters for proteins and nucleic acids
par_all27_prot_lipid.prm all hydrogen parameters for proteins and lipids
param19.inp extended atom parameters for proteins
pardna10_22.inp extended atom parameters for nucleic acids
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, which has
been renamed to stream/toppar_hbond.str. 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 the CHARMM web page at
www.charmm.org, Parameter Set Discussion Forum
ADM Jr., July 2008
www.charmm.org or
http://www.pharmacy.umaryland.edu/faculty/amackere/
References
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
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.
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.
CMAP 2D correction surface
MacKerell, A.D., Jr,. Feig, M., Brooks, C.L., III, Extending the
treatment of backbone energetics in protein force fields: limitations
of gas-phase quantum mechanics in reproducing protein conformational
distributions in molecular dynamics simulations, Journal of
Computational Chemistry, 25: 1400-1415, 2004.
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
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. 2000, 21: 86-104.
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. 2000, 21: 105-120.
Feller, S. and MacKerell, Jr., A.D. An Improved Empirical Potential
Energy Function for Molecular Simulations of Phospholipids, Journal
of Physical Chemistry B, 2000, 104: 7510-7515.
Feller, S. and MacKerell, Jr., A.D. An Improved Empirical Potential
Energy Function for Molecular Simulations of Phospholipids, Journal
of Physical Chemistry B, 2000, 104: 7510-7515.
Klauda, J.B., Brooks, B.R., MacKerell, A.D., Jr., Richard M. Venable,
R.M. and Pastor, R.W., An Ab Initio Study on the Torsional Surface of
Alkanes and its Effect on Molecular Simulations of Alkanes and a DPPC
Bilayer, Journal of Physical Chemistry B, 109; 5300- 5311, 2005
!above references and personal communication from the following
Jeffery Klauda
Joseph O'Connor
Marcus Hadle
Richard Venable
J. Alfredo Freites
Douglas Tobias
Carlos Mondragon-Ramirez
Igor Vorobyov
Alexander D. MacKerell, Jr
Richard W. Pastor
POLYUNSATURATED LIPIDS
Feller, S.E., Gawrisch, K. and MacKerell, Jr., A.D. "Polyunsaturated
Fatty Acids in Lipid Bilayers: Intrinsic and Environmental
Contributions to their Unique Physical Properties,: Journal of the
American Chemical Society, 2002, 124:318-326
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.
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.
Patel, S., MacKerell, A.D., Jr., Brooks, C.L., III, CHARMM fluctuating
charge force field for proteins: II Protein/solvent properties from
molecular dynamics simulations using a nonadditive electrostatic
model, Journal of Computational Chemistry, 25: 1504-1514, 2004
Vorobyov, I., Anisimov, V.M., Greene, S., Venable, R.M., Moser, A.,
Pastor, R.W., and MacKerell, A.D., Jr. "Additive and Classical Drude
Polarizable Force Fields for Linear and Cyclic Ethers," Journal of
Chemical Theory and Computing, 3: 1120-1133, 2007
! O-C-C-O torsion modified
Hwankyu Lee, Richard M Venable, Alexander D MacKerell Jr., Richard W Pastor
Molecular dynamics studies of polyethylene oxide and polyethylene glycol:
Hydrodynamic radius and shape anisotropy
Biophysical J., 95: 1590-1599, 2008
! pyranose monosaccharides
Guvench, O., Greene, S.N., Kamath, G., Brady, J.W., Venable, R.M.,
Pastor, R.W., MacKerell, Jr., A.D. “Additive empirical force field for
hexopyranose monosaccharides” Journal of Computational Chemistry, 29:
2543-2564, 2008. PMID: 18470966
! linear sugars, sugar alcohols, and inositol
Hatcher, E., Guvench, O., and MacKerell, Jr., A.D. “CHARMM Additive
All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates
and Inositol,” Journal of Chemical Theory and Computation, 5:
1315-1327, 2009, DOI: 10.1021/ct9000608.
! hexopyranose glycosidic linkages
Guvench, O., Hatcher, E. R., Venable, R. M., Pastor, R. W., MacKerell,
A. D. Jr. “Additive Empirical CHARMM Force Field for glycosyl linked
hexopyranoses,” Journal of Chemical Theory and Computation, 5,
2353–2370, 2009, DOI: 10.1021/ct900242e
! furanose monosaccharides
Hatcher, E. R.; Guvench, O.; MacKerell, Hatcher, E., Guvench, O., and
MacKerell, Jr., A.D. “CHARMM Additive All-Atom Force Field for
Aldopentofuranose Carbohydrates and Fructofuranose.” Journal of
Physical Chemistry B. 113:12466-76, 2009, PMID: 19694450
!CHARMM GENERAL FORCE FIELD, CGenFF
Vanommeslaeghe, K., Hatcher, E.,Acharya, C., Kundu, S., Zhong, S.,
Shim, J., Darian, E., Guvench, O., Lopes, P., Vorobyov, I. and
Mackerell Jr., A.D., J. Comput. Chem., DOI: 10.1002/jcc.21367