📄 char27_lipid.ff
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# \\\\\\\ CHARMM27 All-Hydrogen Lipid Parameter File ///////# \\\\\\\\\\\\\\\\\\ Developmental /////////////////////////# Alexander D. MacKerell Jr.# September 1998# All comments to ADM jr. email:alex,mmiris.ab.umd.edu# telephone: 410-706-7442# These files are a beta release; additional parameter development# and testing may lead to alteration of the contents.####references##LIPIDS##Schlenkrich, M., Brickmann, J., MacKerell, Jr., A.D., and Karplus, M.#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 and#B. Roux, Eds. Birkhauser, Boston, 1996, pp 31-81.##new ALKANES##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: 334-338.##ALKENES##Feller, S.E., Yin, D., Pastor, R.W., and MacKerell, Jr., A.D.,#Molecular Dynamics Simulation of Unsaturated Lipids at Low Hydration:#Parameterization and Comparison with Diffraction Studies. Biophysical#Journal, 73:2269-2279, 1997.##new PHOSPHATE##MacKerell, Jr., A.D. Influence of Water and Sodium on the Energetics#of Dimethylphosphate and its Implications For DNA Structure, Journal#de Chimie Physique, 1997, 94: 1436-1447.##IONS##all ions from Roux and coworkers## correct alkene dihedral parameters required due to change# in the alkane vdw parameters and apparent discrepancy with# the published surface for 2-butene##BONDS##V(bond) = Kb(b - b0)**2##Kb: kcal/mole/A**2#b0: A##atom type Kb b0#CTL3 CL 1.5220 837.40 ! methyl acetat CTL2 CL 1.5220 837.40 ! methyl acetat CTL1 CL 1.5220 837.40 ! methyl acetat OBL CL 1.2200 3140.25 ! methyl acetat OSL CL 1.3340 628.05 ! methyl acetat OHL CL 1.4000 963.01 ! methyl acetat HOL OHL 0.9600 2281.91 ! acetic aci CTL1 HAL1 1.1110 1293.78 ! alkanes, 3/9 CTL2 HAL2 1.1110 1293.78 ! alkanes, 4/9 CTL3 HAL3 1.1110 1348.21 ! alkanes, 4/9 CTL3 OSL 1.4300 1423.58 ! phosphat CTL2 OSL 1.4300 1423.58 ! phosphat CTL1 OSL 1.4300 1423.58 ! phosphat OSL PL 1.6000 1130.49 ! phosphat O2L PL 1.4800 2428.46 ! phosphat OHL PL 1.5900 992.32 ! phosphat NH3L HCL 1.0400 1716.67 ! ethanolamin NH3L CTL2 1.5100 1092.81 ! ethanolamin NTL CTL2 1.5100 900.20 ! tetramethylammoniu NTL CTL5 1.5100 900.20 ! tetramethylammoniu CTL5 HL 1.0800 1256.10 ! tetramethylammoniu CTL2 HL 1.0800 1256.10 ! tetramethylammoniu CTL1 CTL1 1.5000 931.61 ! alkanes, 3/9 CTL1 CTL2 1.5380 931.61 ! alkanes, 3/9 CTL1 CTL3 1.5380 931.61 ! alkanes, 3/9 CTL2 CTL2 1.5300 931.61 ! alkanes, 3/9 CTL2 CTL3 1.5280 931.61 ! alkanes, 3/9 CTL3 CTL3 1.5300 931.61 ! alkanes, 3/9 OHL CTL1 1.4200 1792.04 ! glycero OHL CTL2 1.4200 1792.04 ! glycero OHL CTL3 1.4200 1792.04 ! glycero SL O2L 1.4480 2260.98 ! methylsulfat SL OSL 1.5750 1046.75 ! methylsulfat HT HT 1.5139 0.00 ! from TIPS3P geometry (for SHAKE w/PARAM HT OT 0.9572 1884.15 ! from TIPS3P geometr CEL2 CEL2 1.3300 2135.37 ! ethene yin,adm jr., 12/9 HEL2 CEL2 1.1000 1528.25 ! propene; from ethene, yin,adm jr., 12/9 CEL1 CTL3 1.5040 1603.62 ! butene, yin,adm jr., 12/9 CEL1 CEL2 1.3420 2093.50 ! propene, yin,adm jr., 12/9 HEL1 CEL1 1.1000 1509.41 ! propene, yin,adm jr., 12/9 CEL1 CTL2 1.5020 1528.25 ! butene; from propene, yin,adm jr., 12/9 CEL1 CEL1 1.3400 1842.28 ! butene, yin,adm jr., 12/9 #ANGLES##V(angle) = Ktheta(Theta - Theta0)**2##V(Urey-Bradley) = Kub(S - S0)**2##Ktheta: kcal/mole/rad**2#Theta0: degrees#Kub: kcal/mole/A**2 (Urey-Bradley)#S0: A##atom types Ktheta Theta0 Kub S0#OBL CL CTL3 125.00 293.09 2.4420 83.74 ! methyl acetatOBL CL CTL2 125.00 293.09 2.4420 83.74 ! methyl acetatOBL CL CTL1 125.00 293.09 2.4420 83.74 ! methyl acetatOSL CL OBL 125.90 376.83 2.2576 669.92 ! acetic aciCL OSL CTL1 109.60 167.48 2.2651 125.61 ! methyl acetatCL OSL CTL2 109.60 167.48 2.2651 125.61 ! methyl acetatCL OSL CTL3 109.60 167.48 2.2651 125.61 ! methyl acetatHAL2 CTL2 CL 109.50 138.17 2.1630 125.61 ! methyl acetatHAL3 CTL3 CL 109.50 138.17 2.1630 125.61 ! methyl acetatCTL2 CTL2 CL 108.000 217.724 ! alkanCTL3 CTL2 CL 108.000 217.724 ! alkanOSL CL CTL3 109.00 230.28 2.3260 83.74 ! methyl acetatOSL CL CTL2 109.00 230.28 2.3260 83.74 ! methyl acetatOHL CL OBL 123.00 209.35 2.2620 879.27 ! acetic aciOHL CL CTL3 110.500 230.285 ! acetic aciOHL CL CTL2 110.500 230.285 ! acetic aciHOL OHL CL 115.000 230.285 ! acetic aciOSL CTL1 CTL2 110.100 316.956 ! acetic aciOSL CTL1 CTL3 110.100 316.956 ! acetic aciOSL CTL2 CTL1 110.100 316.956 ! acetic aciOSL CTL2 CTL2 110.100 316.956 ! acetic aciOSL CTL2 CTL3 110.100 316.956 ! acetic aciHAL2 CTL2 HAL2 109.00 148.64 1.8020 22.61 ! alkane, 3/9HAL3 CTL3 HAL3 108.40 148.64 1.8020 22.61 ! alkane, 3/9HAL1 CTL1 OSL 109.500 251.220 ! phosphatHAL2 CTL2 OSL 109.500 251.220 ! phosphatHAL3 CTL3 OSL 109.500 251.220 ! phosphatCTL2 OSL PL 120.00 83.74 2.3300 146.54 ! phosphatCTL3 OSL PL 120.00 83.74 2.3300 146.54 ! phosphatHOL OHL PL 115.00 125.61 2.3000 167.48 ! phosphatOSL PL OSL 104.300 334.960 ! phosphatOSL PL O2L 111.600 414.094 ! phosphatOSL PL OHL 108.000 201.395 ! phosphatO2L PL O2L 120.000 502.440 ! phosphatO2L PL OHL 108.230 414.094 ! phosphatNTL CTL2 HL 109.50 167.48 2.1300 113.05 ! tetramethylammoniuNTL CTL5 HL 109.50 167.48 2.1300 113.05 ! tetramethylammoniuHL CTL2 HL 109.50 100.49 1.7670 117.24 ! tetramethylammoniuHL CTL5 HL 109.50 100.49 1.7670 117.24 ! tetramethylammoniuCTL5 NTL CTL2 109.50 251.22 2.4660 108.86 ! tetramethylammoniuCTL5 NTL CTL5 109.50 251.22 2.4660 108.86 ! tetramethylammoniuHL CTL2 CTL2 110.10 139.97 2.1790 94.33 ! alkanHL CTL2 CTL3 110.10 139.97 2.1790 94.33 ! alkanHAL1 CTL1 CTL1 110.10 144.45 2.1790 94.33 ! alkane, 3/9HAL1 CTL1 CTL2 110.10 144.45 2.1790 94.33 ! alkane, 3/9HAL1 CTL1 CTL3 110.10 144.45 2.1790 94.33 ! alkane, 3/9HAL2 CTL2 CTL1 110.10 110.96 2.1790 94.33 ! alkane, 4/9HAL2 CTL2 CTL2 110.10 110.96 2.1790 94.33 ! alkane, 4/9HAL2 CTL2 CTL3 110.10 144.87 2.1790 94.33 ! alkane, 4/9HAL3 CTL3 CTL1 110.10 139.97 2.1790 94.33 ! alkane, 4/9HAL3 CTL3 CTL2 110.10 144.87 2.1790 94.33 ! alkane, 4/9HAL3 CTL3 CTL3 110.10 157.01 2.1790 94.33 ! alkane, 4/9NTL CTL2 CTL2 115.000 283.460 ! tetramethylammoniuNTL CTL2 CTL3 115.000 283.460 ! tetramethylammoniuHCL NH3L CTL2 109.50 138.17 2.0560 16.75 ! ethanolaminHCL NH3L HCL 109.500 171.667 ! ethanolaminNH3L CTL2 CTL2 110.000 283.460 ! ethanolaminNH3L CTL2 HAL2 107.50 188.41 2.0836 146.54 ! ethanolaminCTL1 CTL1 CTL1 111.00 223.38 2.5610 33.50 ! alkane, 3/9CTL1 CTL1 CTL2 113.50 244.31 2.5610 46.73 ! glyceroCTL1 CTL1 CTL3 108.50 223.38 2.5610 33.50 ! alkane, 3/9CTL1 CTL2 CTL1 113.50 244.31 2.5610 46.73 ! glyceroCTL1 CTL2 CTL2 113.50 244.31 2.5610 46.73 ! glyceroCTL1 CTL2 CTL3 113.50 244.31 2.5610 46.73 ! glyceroCTL2 CTL1 CTL2 113.50 244.31 2.5610 46.73 ! glyceroCTL2 CTL1 CTL3 113.50 244.31 2.5610 46.73 ! glyceroCTL2 CTL2 CTL2 113.60 244.31 2.5610 46.73 ! alkane, 3/9CTL2 CTL2 CTL3 115.00 242.85 2.5610 33.50 ! alkane, 3/9HOL OHL CTL1 106.000 240.752 ! glyceroHOL OHL CTL2 106.000 240.752 ! glyceroHOL OHL CTL3 106.000 240.752 ! glyceroOHL CTL1 CTL2 110.100 316.956 ! glyceroOHL CTL2 CTL1 110.100 316.956 ! glyceroOHL CTL2 CTL2 110.100 316.956 ! glyceroOHL CTL2 CTL3 110.100 316.956 ! glyceroOHL CTL1 HAL1 108.890 192.183 ! glyceroOHL CTL2 HAL2 108.890 192.183 ! glycero⌨️ 快捷键说明
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