Empirical force field parametrization efforts are coordinated with the program CHARMM, which is maintained in the laboratory of Professor Martin Karplus, Department of Chemistry, Harvard University.

Below is a gzipped tar file containing the topology and parameter files available in version C31B1 of CHARMM.  Note that this release includes a change in the organization of the toppar directory.  The standard topology and parameter files for the biological molecules (e.g. proteins, nucleic acids etc.) have not changed except for a number of the model compounds being moved to toppar stream files.  These files are in the stream subdirectory and are used by first reading the parent topology and parameter files and then streaming the appropriate toppar stream file to add the additional residues, patches and parameters of interest.  This change was motivated by the ever increasing complexity of the topology and parameter files due to the inclusion of additional model compounds.

Topology and parameter files for the AMBER, OPLS and BMS force fields are now included, allowing for modeling studies with CHARMM using these force fields.  See the non_charmm subdirectory.

An overview of the parameter optimization approaches to extend the CHARMM force fields may be found in the following references or in MacKerell, A.D., Jr. "Atomistic Models and Force Fields" in Computational Biochemistry and Biophysics, O.M. Becker, A.D. MacKerell, Jr., B. Roux and M.Watanabe, Eds., Marcel Dekker, Inc. New York, 2001, p. 7-38. 

*See the following link: http://www.dekker.com/servlet/product/productid/0455-X.  Note that the publisher is now Taylor & Francis and the book is available via Amazon.com

* Please reference the parameters as indicated in the individual topology and parameter files.

Topology Files:

toppar_c31b1.tar.gz

Toppar files with c32b1 release of CHARMM. Includes the CMAP extension to the CHARMM22 protein force field and various extensions of the force fields.

toppar_c32b1.tar.gz

Toppar files for trifluoroethanol including example inputs.

toppar_tfe.tar.gz

Supplemental material for Lopes, P.E.M., Murashov, V., Tazi, M., Demchuk, E. and MacKerell, A.D., Jr. "Development of an Empirical Force Field for Silica. Applicaiton to the Quartz-Water Interface." Journal of Physcial Chemistry B, 2006, 110; 2782-2792

jpcb_110_2782_06_supp_mat.tar.gz

Toppar files for ethers:

toppar_ether.tgz

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

and

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., in press (2008)

Dihedral Fitting Procedure:

Guvench, O., MacKerell, A.D., Jr., “Automated conformational energy fitting for force-field developement”, Journal of Molecular Modeling, in press, 2008.

fit_dihedral.tar.gz

Directory for dihedral fitting containing manuscript, input files, python script and readme files.

References To Recently Published Parameter Studies:

Carbohydrates:

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, In Press, 2008.

Kamath, G., Guvench, O., MacKerell, Jr., A.D. “CHARMM Additive All-Atom Force Field for Acyclic Sugars” Jounal of Chemical Theory and Computation, In Press., 2008

toppar_carbo_export_apr08.tgz

Proteins:

Detailed presentation of the new CMAP procedure and its use to treat the conformational properties of the protein backbone:  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.

MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.; Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III, W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M.  All-atom  empirical potential for molecular modeling and dynamics Studies of proteins.  Journal of Physical Chemistry B, 1998, 102, 3586-3616.

Nucleic Acids:

Foloppe, N. and MacKerell, Jr., A.D. "All-Atom Empirical Force Field for Nucleic Acids: 1) Parameter Optimization Based on Small Molecule and Condensed Phase Macromolecular Target Data. Journal of Computational Chemistry, 2000, 21:86-104.

* The supplemental material of  Foloppe and MacKerell is actually the full, unabridged version and can be obtained from http://journals.wiley.com/jcc/. As the published manuscript is an abbreviated version, it is strongly suggested that the full version be obtained in order to get all the details of the parameter optimization procedure.

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 Chemistry, 2000, 21:105-120.  Also see  http://journals.wiley.com/jcc/. for the supplemental material or view versions of Supplemental Material Figure 6a and Figure 6b here.

Lipids:

Schlenkrich, M., Brickmann, J. MacKerell, Jr., A.D. and Karplus, M. An 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, Jr. and B. Roux, Eds. Birkhauser, Boston, 1996.

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.

Biological Macromolecules:

MacKerell, A.D., Jr., Empirical Force Fields for Biological Macromolecules: Overview and Issues, Journal of Computational Chemistry, 25: 1584-1604, 2004

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.  View structures of NAD+ and NADH.

Methods:

Yin, D. and MacKerell, Jr. A.D. Combined Ab initio/Empirical Approach for the Optimization of Lennard-Jones Parameters. Journal of Computational Chemistry, 1998, 19: 334-348.