CHARMM FF Parameters

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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


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


Drude Polarizable Force Field


Additive Force Field Files:


Toppar files with the C37 release of CHARMM. These include the C36 additive protein, nucleic acid, lipid, and carbohydrate releases as well as the CGenFF files as of July 2012. Note that the toppar files are now in a new format that allows them to be read individually such that different parts of the force field (eg. proteins and nucleic acids) can be accessed without creating toppar files that contain both the protein and nucleic acid parameters. Note that this includes a toppar stream file for water and ions that must be explicitly read as water and the ions are no longer included in the biomolecular or CGenFF toppar files. See 00toppar_file_format.txt, included in the .tgz file, for details including an example on how to read the files into CHARMM.



Note that the replacement of toppar_c36_aug12.tgz with toppar_c36_dec13.tgz involved a change in the ordering of atoms in selected residues and an update of the carbohydrate parameters.


toppar_c36_dec13.tgz



CHARMM36 force field in Gromacs format.


charmm36-mar2014.ff.tgz



A Python program to convert ParamChem CGenFF toppar stream file from CHARMM to Gromacs format. The comments section in the beginning of the program provides usage information.


cgenff_charmm2gmx.py



Toppar files with c35b2, c36a2 release of CHARMM.


toppar_c35b2_c36a2.tgz


Toppar files for CHARMM36 all-atom carbohydrate force field.


toppar_carb_apr12.tgz


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 with c31b1 release of CHARMM.


toppar_c31b1.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, J Mol Model (2008) 14:667-679.


fit_dihedral.tar.gz


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



References To Recently Published Parameter Studies:


General FF:

K. Vanommeslaeghe, E. Hatcher, C. Acharya, S. Kundu, S. Zhong, J. Shim, E. Darian, O. Guvench, P. Lopes, I. Vorobyov, A. D. MacKerell Jr., CHARMM General Force Field (CGenFF): "A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields", Journal of Computational Chemistry 2010, 31, 671-690.


Before downloading please read this warning!

toppar_all36a_cgenff.tgz

The force field can automatically be applied to an arbitrary organic molecule using the CGenFF program, which can be accessed through the ParamChem website. Click here for usage information. The resulting parameters and charges are accompanied by penalty scores. If these penalty scores are high, it is recommended to re-optimize the parameters, as described in the above reference and the tutorial.


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.


Lipid C36 all-atom additive parameters:

Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph W. O'Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, Jr. and Richard W. Pastor ""Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types", J. Phys. Chem. B, Articles, ASAP (As Soon As Publishable) Publication Date (Web): May 24, 2010, (Article), DOI: 10.1021/jp101759q.


toppar_lipid_all36.tgz


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.