1 2 3CHARMM36 EEF1-SB all-atom force field (May 2015) 4 5******************************************************************************* 6* CHARMM36 port writted by * 7* E. Prabhu Raman, Justin A. Lemkul, Robert Best * 8* and Alexander D. MacKerell, Jr. * 9* CHARMM force field homepage: * 10* www.mackerell.umaryland.edu/CHARMM_ff_params.html * 11******************************************************************************* 12 13Parameters taken from CHARMM36 and CGenFF 3.0.1 14 Included are topologies from 15 top_all36_prot.rtf 16 top_all36_na.rtf 17 top_all36_lipid.rtf 18 top_all36_carb.rtf 19 top_all36_cgenff.rtf 20 top_all35_ethers.rtf 21 and corresponding prm files 22 23References: 24 25** Proteins 26 27Best, R. B. et al. Optimization of the Additive CHARMM All-Atom Protein 28Force Field Targeting Improved Sampling of the Backbone phi, psi and Side-Chain 29chi1 and chi2 Dihedral Angles, Journal of Chemical Theory and Computation, 302012, 8: 3257-3273. 31 32MacKerell, Jr., A.D., Feig, M., Brooks, III, C.L. Extending the 33treatment of backbone energetics in protein force fields: limitations 34of gas-phase quantum mechanics in reproducing protein conformational 35distributions in molecular dynamics simulations, Journal of 36Computational Chemistry, 2004, 25: 1400-1415. 37 38MacKerell, Jr., A.D., et al. All-atom empirical potential for 39molecular modeling and dynamics Studies of proteins, Journal of 40Physical Chemistry B, 1998, 102, 3586-3616. 41 42! phosphotyrosine 43Feng, M.-H., Philippopoulos, M., MacKerell, Jr., A.D. and Lim, C. 44Structural Characterization of the Phosphotyrosine Binding Region of a 45High-Affinity aSH2 Domain-Phosphopeptide Complex by Molecular Dynamics 46Simulation and Chemical Shift Calculations. Journal of the American 47Chemical Society, 1996, 118: 11265-11277. 48 49** Lipids 50 51Klauda, J. B. et al. Improving the CHARMM Force Field for Polyunsaturated 52Fatty Acid Chains, Journal of Physical Chemistry B, 2012, 116: 9424-9431. 53 54Klauda, J. B. et al. Update of the CHARMM All-Atom Additive Force Field 55for Lipids: Validation on Six Lipid Types, Journal of Physical Chemistry B, 562010, 114: 7830-7843. 57 58Feller, S. and MacKerell, Jr., A.D. An Improved Empirical Potential 59Energy Function for Molecular Simulations of Phospholipids, Journal 60of Physical Chemistry B, 2000, 104: 7510-7515. 61 62! cholesterol 63Lim, J.B., Rogaski, B. and Klauda, J.B.. "Update of the Cholesterol Force Field 64Parameters in CHARMM" 116: 203-210 (2012). 65 66! bacterial lipids 67Lim, J.B. & Klauda, J.B. Branching at the Iso- and Anteiso- Positions in Complex Chlamydia 68Membranes: A Molecular Dynamics Study. Biochimica et Biophysica Acta (BBA) - Biomembranes 691808:323-331 (2011). 70 71Pandit, K.R. & Klauda, J.B. Membrane models of E. coli containing cyclic moieties in 72the aliphatic lipid chain. Biochimica et Biophysica Acta (BBA) - Biomembranes 731818:1205-1210 (2012). 74 75** Nucleic Acids 76 77Denning, E.J., Priyakumar, U.D., Nilsson, L., and MacKerell Jr., A.D., 78"Impact of 2'-hydroxyl sampling on the conformational properties of 79RNA: Update of the CHARMM all-atom additive force field for RNA," 80JCC, 32: 1929-1943, 2011, PMC3082605 81 82Hart, K., Foloppe, N., Baker, C.M., Denning, E.J., Nilsson, L. 83and MacKerell Jr., A.D. "Optimization of the CHARMM additive force 84field for DNA: Improved treatment of the BI/BII conformational 85equilibrium," JCTC, 8:348-362, 2012, PMC3285246 86 87** Carbohydrates 88 89! pyranose monosaccharides 90Guvench, O., Greene, S.N., Kamath, G., Brady, J.W., Venable, R.M., 91Pastor, R.W., MacKerell, Jr., A.D. "Additive empirical force field for 92hexopyranose monosaccharides," Journal of Computational Chemistry, 29: 932543-2564, 2008. PMID: 18470966 94 95! linear sugars, sugar alcohols, and inositol 96Hatcher, E., Guvench, O., and MacKerell, Jr., A.D. "CHARMM Additive 97All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates 98and Inositol," Journal of Chemical Theory and Computation, 5: 991315-1327, 2009, DOI: 10.1021/ct9000608. 100 101! hexopyranose glycosidic linkages 102Guvench, O., Hatcher, E. R., Venable, R. M., Pastor, R. W., MacKerell, Jr., 103A. D. "Additive Empirical CHARMM Force Field for glycosyl linked 104hexopyranoses," Journal of Chemical Theory and Computation, 5, 1052353-2370, 2009, DOI: 10.1021/ct900242e 106 107! furanose monosaccharides 108Hatcher, E. R.; Guvench, O. and MacKerell, Jr., A.D. 109"CHARMM Additive All-Atom Force Field for Aldopentofuranose 110Carbohydrates and Fructofuranose." Journal of Physical Chemistry B. 111113:12466-76, 2009, PMID: 19694450 112 113! glycosidic linkages involving furanoses 114Raman, E. P., Guvench, O., MacKerell, Jr., A.D., "CHARMM Additive All-Atom 115Force Field for Glycosidic Linkages in Carbohydrates Involving Furanoses," 116Journal of Physical Chemistry B, 114: 12981-12994, 2010, PMID: 20845956 117 118! carbohydrate derivatives and glycosidic linkages for glycoproteins 119Guvench, O., Mallajosyula, S.S. Raman, E.P., Hatcher, E. Vanommeslaeghe, K., 120Foster, T.J., Jamison II, F.W., and MacKerell, Jr., A.D. "CHARMM additive 121all-atom force field for carbohydrate derivatives and their utility in 122polysaccharide and carbohydrate-protein modeling," JCTC, 7: 3162-3180, 2011. 123PMC3224046 124 125!O-glycan linkages 126Mallajosyula, S. S. and MacKerell, Jr., A.D., "Influence of Solvent and 127Intramolecular Hydrogen Bonding on the Conformational Properties of O-Linked 128Glycopeptides," Journal of Physical Chemistry B, 115: 11215-11229, 2011 129PMC3224046 130 131! Phosphates and sulfates 132Mallajosyula, S. S.; Guvench, O.; Hatcher, E. R. and MacKerell, Jr., A.D., 133CHARMM Additive All-Atom Force Field for Phosphate and Sufate Linkages in 134carbohydrates" JCTC, 8: 759-776, 2012. 135 136** CHARMM General Force Field 137 138Vanommeslaeghe, K. et al. CHARMM General Force Field: A Force Field for Drug-Like 139Molecules Compatible with the CHARMM All-Atom Additive Biological Force Fields, 140Journal of Computational Chemistry, 2010, 31: 671-690. 141 142W. Yu, X. He, K. Vanommeslaeghe, A. D. MacKerell Jr. Extension of the CHARMM general force field to sulfonyl-containing compounds and its utility in biomolecular simulations, J. Comput. Chem. 2012, 33, 2451-2468. 143 144** Implementation of CHARMM in GROMACS 145 146Bjelkmar, P., Larsson, P., Cuendet, M. A, Bess, B., Lindahl, E. 147Implementation of the CHARMM force field in GROMACS: Analysis of protein 148stability effects from correction maps, virtual interaction sites, and 149water models, Journal of Chemical Theory and Computation, 2010, 6: 459-466. 150 151 152 153