CHARMM Force Field Files

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CHARMM Additive Force Field Files
CHARMM Drude Force Field Files
CHARMM36 Files for GROMACS
CHARMM36 Files for Anton
References

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

Below gzipped tar files containing the topology and parameter files available various releases of CHARMM. Note that as of the C31B1 release the organization of the toppar directory was changed. 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 subdirectories 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.

Selected opology and parameter files for the AMBER, OPLS and BMS force fields are now included, allowing for modeling studies with CHARMM using these force fields. In addition, parameters for a number of more recent water models are available. 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, Jr., A.D. "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.


Additive Force Field Files

Toppar files included with C37 and later versions of CHARMM include the C36 additive protein, nucleic acid, lipid, and carbohydrate releases as well as the CGenFF files. 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. 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.



The July 2016 update of the c36 toppar files includes changing the MASS atom type number specifications to "MASS -1" associated with code developments in CHARMM that allow atom type numbers to be assigned as they are read. This is compatible with version C39 onward and does not impact the default PSF format (the XPLOR format) that may be read into NAMD and other programs. A version of the toppar files, toppar_c36_jul16_mass_orig.tgz, with the old mass numbers is available for back compatibility. In addition, note the modified C36 protein parameter set, par_all36m_prot.prm, that corrects oversampling of the alphaL conformation and gives improved sampling of disordered states of peptides. These parameters, in conjunction with top_all36_prot.rtf, should be used for all simulations involving peptides and proteins.

toppar_c36_jul16.tgz

toppar_c36_jul16_mass_orig.tgz

The February 2016 update of the c36 toppar files involves extensions of the force field to include modified RNA bases and nucleotides that occur in tRNA and other systems, a modified C36 protein parameter set that corrects oversampling of the alphaL conformation and gives improved sampling of disordered states of peptides and the addition of sulfamate to the carbohydrate parameters to allow simulations of heparin and related glycans.

toppar_c36_feb16.tgz

The August 2015 update of the c36 toppar files involves extensions of the force field to include selected posttranslational modifications, additional lipids and carbohydrates and a comprehensive set of ion parameters (stream/misc/toppar_ions_won.str).

toppar_c36_aug15.tgz

Note that the replacement of toppar_c36_dec13.tgz with toppar_c36_aug14.tgz involved moving the toppar stream files into subdirectories for each class of biomolecules, addition of stream files for different water models in the non_charmm subdirectory, patches for ionized cysteine and serine and an update of the lipid toppar stream files to maintain consistency with those supported by the CHARMM-Gui.

toppar_c36_aug14.tgz

This link points to the version of the all-atom CGenFF additive parameter set that is compatible with cgenff.paramchem.org. Older versions can be obtained from the CGenFF download page, which also hosts the change logs. See the references section for more info.

toppar_all36a_cgenff.tgz

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, Jr., A.D. "Development of an Empirical Force Field for Silica. Application to the Quartz-Water Interface," Journal of Physcial Chemistry B 110: 2782-2792, 2006.

jpcb_110_2782_06_supp_mat.tar.gz

Toppar files for ethers:

Vorobyov, I., Anisimov, V.M., Greene, S., Venable, R.M., Moser, A., Pastor, R.W., and MacKerell, Jr., A.D.. "Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers," Journal of Chemical Theory and Computation 3: 1120-1133, 2007.

and

Lee, H., Venable, R.M., MacKerell, Jr., A.D., and Pastor, R.W. "Molecular dynamics studies of polyethylene oxide and polyethylene glycol: Hydrodynamic radius and shape anisotropy," Biophysical Journal 95: 1590-1599, 2008.

toppar_ether.tgz



CHARMM36 Files for GROMACS

CHARMM36 force field in GROMACS format, including CGenFF version 4.0. Updated November 2016.

charmm36-nov2016.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



CHARMM36 Files for Anton

The vippar utility contains updated CHARMM36 force field for running MD simulations on Anton. However, the default vippar charmm36_lipid directory uses the c36c model (JPCB, 2011, 166, 203) for cholesterol. This model uses CGenFF atom types and contains NBFix terms that, when too numerous, cause Anton error messages. It is highly suggested to use the following CHARMM36 lipid force field where cholesterol toppology and parameters are rolled back to the original c36 model (Biochemistry, 2004, 43, 15318) while all other lipids are kept the same.

charmm36_lipids_c36chl1.tar.gz

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

cgenff_charmm2anton.py



References for the all-atom additive CHARMM force fields

CHARMM General FF (CGenFF)

Vanommeslaeghe, K. Hatcher, E. Acharya, C. Kundu, S. Zhong, S. Shim, J. E. Darian, E. Guvench, O. Lopes, P. Vorobyov, I. and MacKerell, Jr. A.D. "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 31: 671-90, 2010, PMC2888302 [DOI]

Vanommeslaeghe, K., and MacKerell Jr., A.D., "Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing," Journal of Chemical Informationa and Modeling, 52: 3144-3154, 2012, PMC3528824 [DOI]

Vanommeslaeghe, K., Raman, E.P., and MacKerell Jr., A.D., "Automation of the CHARMM General Force Field (CGenFF) II: Assignment of bonded parameters and partial atomic charges, Journal of Chemical Informationa and Modeling, 52: 3155-3168, 2012, PMC3528813 [DOI]

Yu, W., He, X., Vanommeslaeghe, K. and MacKerell, A.D., Jr., "Extension of the CHARMM General Force Field to Sulfonyl-Containing Compounds and Its Utility in Biomolecular Simulations," Journal of Computational Chemistry, 33: 2451-2468, 2012, PMC3477297 [DOI]

Soteras Gutierrez, I., Lin, F.-Y., Vanommeslaeghe, K., Lemkul, J.A., Armacost, K.A., Brooks, Cl., III, and MacKerell, A.D., Jr., "Parametrization of Halogen Bonds in the CHARMM General Force Field: Improved treatment of ligand-protein interactions," Bioorganic & Medicinal Chemistry, In Press, 2016, [DOI]

The force field can automatically be applied to an arbitrary organic molecule using the CGenFF program, which can be conveniently be accessed through the cgenff.paramchem.org web interface. 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.

The CGenFF topology and parameter files are included with the full release of the CHARMM additive toppar files. Before downloading and using CGenFF please read this warning!

Frequent users of the CGenFF program may wish to obtain a binary license. The procedure for obtaining a free-of-charge not-for-profit license is initiated by e-mailing us; it may take up to a few weeks and will require someone with signature authority at your institution to sign a license agreement that needs to be sent back to us.

For-profit users may obtain the CGenFF program from SilcsBio, LLC.



Proteins

C36m Protein

  • Huang, J., Rauscher, S., Nawrocki, G., Ran, T., Feig, M, de Groot, B.L., Grubmuller, H., and MacKerell, A.D., Jr., "CHARMM36m: An Improved Force Field for Folded and Intrinsically Disordered Proteins," Nature Methods, 14:71-73, 2016, PMC5199616,[DOI]
  • C36 Protein

  • Best, R.B., Zhu, X., Shim, J., Lopes, P.E.M., Mittal, J., Feig, M., and MacKerell Jr., A.D. "Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone phi, psi and side-chain chi1 and chi2 dihedral angles," Journal of Chemical Theory and Computation, 8: 3257-3273, 2012, PMC3549273 [DOI]
  • C22/CMAP

  • 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., ad Karplus, M. "All-atom empirical potential for molecular modeling and dynamics studies of proteins," Journal of Physical Chemistry B 102: 3586-3616, 1998 [DOI]
  • MacKerell, Jr., A.D., Feig, M., and Brooks, III, C.L. "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. [DOI]


  • Nucleic Acids

    C36 DNA

  • Hart, K., Foloppe, N., Baker, C.M., Denning, E.J., Nilsson, L. and MacKerell, A.D., Jr., "Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium," Journal of Chemical Theory and Computation, 8: 348-362, 2012, [DOI] PMC3285246
  • C36 RNA

  • Denning, E.J. Priyakumar, U.D. Nilsson, L. and MacKerell, Jr. A.D. "Impact of 2'-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA," Journal of Computational Chemistry 32: 1929-1943, 2011, [DOI]
  • C27 RNA and DNA

  • 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 21: 86-104, 2000, [DOI]
  • 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 21: 105-120, 2000. [DOI] Also see http://journals.wiley.com/jcc/ for the supplemental material or view versions of Supplemental Material Figure 6a and Figure 6b here.


  • Lipids

    C36 lipids

  • Klauda, J.B., Venable, R.M., Freites, J.A., O'Connor, J.W., Tobias, D.J., Mondragon-Ramirez, C., Vorobyov, I., MacKerell, Jr., A.D., and Pastor, R.W. "Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types," Journal of Physical Chemistry B, 114: 7830-7843, 2010, [DOI]
  • C22 and C27 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 73: 2269-2279, 1997.


  • Carbohydrates

  • Guvench, O., Mallajosyula, S.S. Raman, E.P., Hatcher, E. Vanommeslaeghe, K., Foster, T.J., Jamison II, F.W., and MacKerell, A.D., Jr. "CHARMM additive all-atom force field for carbohydrate derivatives and their utility in polysaccharide and carbohydrate-protein modeling," Journal of Chemical Theory and Computing, 7: 3162-3180, 2011, [DOI], PMC3224046
  • Mallajosyula, S.S., Guvench, O., Hatcher, E., MacKerell, A.D., Jr., "CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked to Carbohydrates," Journal of Chemical Theory and Computation, 8: 759-776, 2012, [DOI], PMC3367516
  • Raman, P. Guvench, O. MacKerell, Jr. A.D. "CHARMM Additive All-Atom Force Field for Glycosidic Linkages in Carbohydrates Involving Furanoses," Journal of Physical Chemistry B 114: 12981-12994, 2010, [DOI], PMC2958709
  • Guvench, O. Hatcher, E.R. Venable, R.M. Pastor, R.W. and MacKerell Jr., A.D. "Additive Empirical CHARMM Force Field for glycosyl linked hexopyranoses," Journal of Chemical Theory and Computation 5: 2353-2370, 2009, [DOI], PMC2757763


  • Empirical Force Field Reviews

  • MacKerell, Jr., A.D. "Empirical Force Fields for Biological Macromolecules: Overview and Issues," Journal of Computational Chemistry 25: 1584-1604, 2004, [DOI]
  • Lopes, P.E.M., Guvench, O., and MacKerell, A.D., Jr., Current Status of Protein Force Fields for Molecular Dynamics, In Molecular Modeling of Proteins, 2nd edition, A. Kukol, Editor, Humana Press. Chapter 3, pp. 47 -72, 2014, [DOI], (Methods in Molecular Biology, 1215: 47-72, 2014).
  • Guvench, O. and MacKerell, Jr. A.D. "Comparison of protein force fields for molecular dynamics simulations," In Molecular Modeling of Proteins, A. Kukol, Ed. Humana Press, Humana Press. 2008 (Methods Mol Biol. 2008;443:63-88. PMID: 18446282)


  • Methods

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





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