* \\\\\\\ CHARMM27 All-Hydrogen Lipid Parameter File /////// * \\\\\\\\\\\\\\\\\\ Developmental ///////////////////////// * Alexander D. MacKerell Jr. * August 1999 * All comments to ADM jr. email:alex,mmiris.ab.umd.edu * telephone: 410-706-7442 * !references ! !LIPIDS ! !Feller, S. and MacKerell, Jr., A.D. manuscript in preparation ! !and ! !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 ! !Sodium ! !Beglov, D. and Roux, B., Finite Representation of an Infinite !Bulk System: Solvent Boundary Potential for Computer Simulations, !Journal of Chemical Physics, 1994, 100: 9050-9063 ! BONDS ! !V(bond) = Kb(b - b0)**2 ! !Kb: kcal/mole/A**2 !b0: A ! !atom type Kb b0 ! CTL3 CL 200.0 1.522 ! methyl acetate CTL2 CL 200.0 1.522 ! methyl acetate CTL1 CL 200.0 1.522 ! methyl acetate OBL CL 750.0 1.220 ! methyl acetate OCL CL 525.0 1.260 ! acetate, protein OSL CL 150.0 1.334 ! methyl acetate OHL CL 230.0 1.40 ! methyl acetate HOL OHL 545.0 0.960 ! acetic acid CTL1 HAL1 309.00 1.111 ! alkanes, 3/92 CTL2 HAL2 309.00 1.111 ! alkanes, 4/98 CTL3 HAL3 322.00 1.111 ! alkanes, 4/98 CTL3 OSL 340.0 1.43 ! phosphate CTL2 OSL 340.0 1.43 ! phosphate CTL1 OSL 340.0 1.43 ! phosphate OSL PL 270.0 1.60 ! phosphate O2L PL 580.0 1.48 ! phosphate OHL PL 237.0 1.59 ! phosphate NH3L HCL 410.0 1.04 ! ethanolamine NH3L CTL2 261.0 1.51 ! ethanolamine NTL CTL2 215.00 1.51 ! tetramethylammonium NTL CTL5 215.00 1.51 ! tetramethylammonium CTL5 HL 300.00 1.08 ! tetramethylammonium CTL2 HL 300.00 1.08 ! tetramethylammonium CTL1 CTL1 222.500 1.500 ! alkanes, 3/92 CTL1 CTL2 222.500 1.538 ! alkanes, 3/92 CTL1 CTL3 222.500 1.538 ! alkanes, 3/92 CTL2 CTL2 222.500 1.530 ! alkanes, 3/92 CTL2 CTL3 222.500 1.528 ! alkanes, 3/92 CTL3 CTL3 222.500 1.530 ! alkanes, 3/92 OHL CTL1 428.0 1.420 ! glycerol OHL CTL2 428.0 1.420 ! glycerol OHL CTL3 428.0 1.420 ! glycerol SL O2L 540.0 1.448 ! methylsulfate SL OSL 250.0 1.575 ! methylsulfate HT HT 0.0 1.5139 ! from TIPS3P geometry (for SHAKE w/PARAM) HT OT 450.0 0.9572 ! from TIPS3P geometry CEL2 CEL2 510.000 1.330 ! ethene yin,adm jr., 12/95 HEL2 CEL2 365.000 1.100 ! propene; from ethene, yin,adm jr., 12/95 CEL1 CTL3 383.000 1.504 ! butene, yin,adm jr., 12/95 CEL1 CEL2 500.000 1.342 ! propene, yin,adm jr., 12/95 HEL1 CEL1 360.500 1.100 ! propene, yin,adm jr., 12/95 CEL1 CTL2 365.000 1.502 ! butene; from propene, yin,adm jr., 12/95 CEL1 CEL1 440.000 1.340 ! butene, yin,adm jr., 12/95 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 70.0 125.0 20.0 2.442 ! methyl acetate OBL CL CTL2 70.0 125.0 20.0 2.442 ! methyl acetate OBL CL CTL1 70.0 125.0 20.0 2.442 ! methyl acetate OSL CL OBL 90.0 125.9 160.0 2.2576 ! acetic acid CL OSL CTL1 40.0 109.6 30.0 2.2651 ! methyl acetate CL OSL CTL2 40.0 109.6 30.0 2.2651 ! methyl acetate CL OSL CTL3 40.0 109.6 30.0 2.2651 ! methyl acetate HAL2 CTL2 CL 33.00 109.50 30.00 2.163 ! methyl acetate HAL3 CTL3 CL 33.00 109.50 30.00 2.163 ! methyl acetate CTL2 CTL2 CL 52.0 108.00 ! alkane CTL3 CTL2 CL 52.0 108.00 ! alkane OSL CL CTL3 55.0 109.0 20.00 2.3260 ! methyl acetate OSL CL CTL2 55.0 109.0 20.00 2.3260 ! methyl acetate OHL CL OBL 50.0 123.0 210.0 2.2620 ! acetic acid OCL CL CTL2 40.0 118.0 50.0 2.3880 ! acetate OCL CL CTL3 40.0 118.0 50.0 2.3880 ! acetate OCL CL OCL 100.0 124.0 70.0 2.2250 ! acetate OHL CL CTL3 55.0 110.50 ! acetic acid OHL CL CTL2 55.0 110.50 ! acetic acid HOL OHL CL 55.0 115.0 ! acetic acid OSL CTL1 CTL2 75.700 110.10 ! acetic acid OSL CTL1 CTL3 75.700 110.10 ! acetic acid OSL CTL2 CTL1 75.700 110.10 ! acetic acid OSL CTL2 CTL2 75.700 110.10 ! acetic acid OSL CTL2 CTL3 75.700 110.10 ! acetic acid HAL2 CTL2 HAL2 35.500 109.00 5.40 1.80200 ! alkane, 3/92 HAL3 CTL3 HAL3 35.500 108.40 5.40 1.80200 ! alkane, 3/92 HAL1 CTL1 OSL 60.0 109.5 ! phosphate HAL2 CTL2 OSL 60.0 109.5 ! phosphate HAL3 CTL3 OSL 60.0 109.5 ! phosphate CTL2 OSL PL 20.0 120.0 35.0 2.33 ! phosphate CTL3 OSL PL 20.0 120.0 35.0 2.33 ! phosphate HOL OHL PL 30.0 115.0 40.0 2.30 ! phosphate OSL PL OSL 80.0 104.3 ! phosphate OSL PL O2L 98.9 111.6 ! phosphate OSL PL OHL 48.1 108.0 ! phosphate O2L PL O2L 120.0 120.0 ! phosphate O2L PL OHL 98.9 108.23 ! phosphate NTL CTL2 HL 40.0 109.5 27. 2.13 ! tetramethylammonium NTL CTL5 HL 40.0 109.5 27. 2.13 ! tetramethylammonium HL CTL2 HL 24.0 109.50 28. 1.767 ! tetramethylammonium HL CTL5 HL 24.0 109.50 28. 1.767 ! tetramethylammonium CTL5 NTL CTL2 60.0 109.5 26. 2.466 ! tetramethylammonium CTL5 NTL CTL5 60.0 109.5 26. 2.466 ! tetramethylammonium HL CTL2 CTL2 33.430 110.10 22.53 2.179 ! alkane HL CTL2 CTL3 33.430 110.10 22.53 2.179 ! alkane HAL1 CTL1 CTL1 34.500 110.10 22.53 2.179 ! alkane, 3/92 HAL1 CTL1 CTL2 34.500 110.10 22.53 2.179 ! alkane, 3/92 HAL1 CTL1 CTL3 34.500 110.10 22.53 2.179 ! alkane, 3/92 HAL2 CTL2 CTL1 26.500 110.10 22.53 2.179 ! alkane, 4/98 HAL2 CTL2 CTL2 26.500 110.10 22.53 2.179 ! alkane, 4/98 HAL2 CTL2 CTL3 34.600 110.10 22.53 2.179 ! alkane, 4/98 HAL3 CTL3 CTL1 33.430 110.10 22.53 2.179 ! alkane, 4/98 HAL3 CTL3 CTL2 34.600 110.10 22.53 2.179 ! alkane, 4/98 HAL3 CTL3 CTL3 37.500 110.10 22.53 2.179 ! alkane, 4/98 NTL CTL2 CTL2 67.7 115.00 ! tetramethylammonium NTL CTL2 CTL3 67.7 115.00 ! tetramethylammonium HCL NH3L CTL2 33.0 109.50 4.00 2.056 ! ethanolamine HCL NH3L HCL 41.0 109.50 ! ethanolamine NH3L CTL2 CTL2 67.7 110.00 ! ethanolamine NH3L CTL2 HAL2 45.0 107.50 35.00 2.0836 ! ethanolamine CTL1 CTL1 CTL1 53.350 111.00 8.00 2.561 ! alkane, 3/92 CTL1 CTL1 CTL2 58.350 113.50 11.16 2.561 ! glycerol CTL1 CTL1 CTL3 53.350 108.50 8.00 2.561 ! alkane, 3/92 CTL1 CTL2 CTL1 58.350 113.50 11.16 2.561 ! glycerol CTL1 CTL2 CTL2 58.350 113.50 11.16 2.561 ! glycerol CTL1 CTL2 CTL3 58.350 113.50 11.16 2.561 ! glycerol CTL2 CTL1 CTL2 58.350 113.50 11.16 2.561 ! glycerol CTL2 CTL1 CTL3 58.350 113.50 11.16 2.561 ! glycerol CTL2 CTL2 CTL2 58.350 113.60 11.16 2.561 ! alkane, 3/92 CTL2 CTL2 CTL3 58.000 115.00 8.00 2.561 ! alkane, 3/92 HOL OHL CTL1 57.500 106.00 ! glycerol HOL OHL CTL2 57.500 106.00 ! glycerol HOL OHL CTL3 57.500 106.00 ! glycerol OHL CTL1 CTL2 75.700 110.10 ! glycerol OHL CTL2 CTL1 75.700 110.10 ! glycerol OHL CTL2 CTL2 75.700 110.10 ! glycerol OHL CTL2 CTL3 75.700 110.10 ! glycerol OHL CTL1 HAL1 45.900 108.89 ! glycerol OHL CTL2 HAL2 45.900 108.89 ! glycerol OHL CTL3 HAL3 45.900 108.89 ! glycerol O2L SL O2L 130.0 109.47 35.0 2.45 ! methylsulfate O2L SL OSL 85.0 98.0 ! methylsulfate CTL2 OSL SL 15.0 109.0 27.00 1.90 ! methylsulfate CTL3 OSL SL 15.0 109.0 27.00 1.90 ! methylsulfate HT OT HT 55.0 104.52 ! FROM TIPS3P GEOMETRY CEL1 CEL1 CTL2 48.00 123.50 ! from 2-butene, yin,adm jr., 12/95 CEL1 CEL1 CTL3 48.00 123.50 ! 2-butene, yin,adm jr., 12/95 CEL2 CEL1 CTL2 48.00 126.00 ! 1-butene; from propene, yin,adm jr., 12/95 CEL2 CEL1 CTL3 47.00 125.20 ! propene, yin,adm jr., 12/95 HEL1 CEL1 CEL1 52.00 119.50 ! 2-butene, yin,adm jr., 12/95 HEL1 CEL1 CEL2 42.00 118.00 ! propene, yin,adm jr., 12/95 HEL1 CEL1 CTL2 40.00 116.00 ! 1-butene; from propene, yin,adm jr., 12/95 HEL1 CEL1 CTL3 22.00 117.00 ! propene, yin,adm jr., 12/95 HEL2 CEL2 CEL1 45.00 120.50 ! propene, yin,adm jr., 12/95 HEL2 CEL2 CEL2 55.50 120.50 ! ethene, yin,adm jr., 12/95 HEL2 CEL2 HEL2 19.00 119.00 ! propene, yin,adm jr., 12/95 CEL1 CTL2 CTL2 32.00 112.20 ! 1-butene; from propene, yin,adm jr., 12/95 CEL1 CTL2 CTL3 32.00 112.20 ! 1-butene; from propene, yin,adm jr., 12/95 HAL2 CTL2 CEL1 45.00 111.50 ! 1-butene; from propene, yin,adm jr., 12/95 HAL3 CTL3 CEL1 42.00 111.50 ! 2-butene, yin,adm jr., 12/95 DIHEDRALS ! !V(dihedral) = Kchi(1 + cos(n(chi) - delta)) ! !Kchi: kcal/mole !n: multiplicity !delta: degrees ! !atom types Kchi n delta ! X CTL1 OHL X 0.14 3 0.00 ! glycerol X CTL2 OHL X 0.14 3 0.00 ! glycerol X CTL3 OHL X 0.14 3 0.00 ! glycerol OBL CL CTL2 HAL2 0.00 6 180.00 ! acetic acid OBL CL CTL3 HAL3 0.00 6 180.00 ! acetic acid OSL CL CTL2 HAL2 0.00 6 180.00 ! acetic acid OSL CL CTL3 HAL3 0.00 6 180.00 ! acetic acid OBL CL OSL CTL1 0.965 1 180.00 ! methyl acetate OBL CL OSL CTL1 3.85 2 180.00 ! methyl acetate OBL CL OSL CTL2 0.965 1 180.00 ! methyl acetate OBL CL OSL CTL2 3.85 2 180.00 ! methyl acetate OBL CL OSL CTL3 0.965 1 180.00 ! methyl acetate OBL CL OSL CTL3 3.85 2 180.00 ! methyl acetate X CL OSL X 2.05 2 180.00 ! methyl acetate X CTL2 CL X 0.05 6 180.00 ! methyl acetate X CTL3 CL X 0.05 6 180.00 ! methyl acetate X CL OHL X 2.05 2 180.00 ! acetic acid HAL2 CTL2 CL OHL 0.00 6 180.00 HAL3 CTL3 CL OHL 0.00 6 180.00 OSL PL OSL CTL2 1.20 1 180.00 ! phosphate, new NA, 4/98, adm jr. OSL PL OSL CTL2 0.10 2 180.00 ! phosphate, new NA, 4/98, adm jr. OSL PL OSL CTL2 0.10 3 180.00 ! phosphate, new NA, 4/98, adm jr. O2L PL OSL CTL2 0.10 3 0.00 ! phosphate, new NA, 4/98, adm jr. OSL PL OSL CTL3 1.20 1 180.00 ! phosphate, new NA, 4/98, adm jr. OSL PL OSL CTL3 0.10 2 180.00 ! phosphate, new NA, 4/98, adm jr. OSL PL OSL CTL3 0.10 3 180.00 ! phosphate, new NA, 4/98, adm jr. O2L PL OSL CTL3 0.10 3 0.00 ! phosphate, new NA, 4/98, adm jr. OHL PL OSL CTL2 0.95 2 0.00 ! terminal phosphate OHL PL OSL CTL2 0.50 3 0.00 ! terminal phosphate OHL PL OSL CTL3 0.95 2 0.00 ! terminal phosphate OHL PL OSL CTL3 0.50 3 0.00 ! terminal phosphate X OHL PL X 0.30 3 0.00 ! terminal phosphate X CTL1 OSL X 0.00 3 0.00 ! phosphate, new NA, 4/98, adm jr. X CTL2 OSL X 0.00 3 0.00 ! phosphate, new NA, 4/98, adm jr. X CTL3 OSL X 0.00 3 0.00 ! phosphate, new NA, 4/98, adm jr. CTL3 CTL2 OSL CL 0.7 1 180.00 ! ethyl acetate, 12/92 CTL2 CTL2 OSL CL 0.7 1 180.00 ! ethyl acetate, 12/92 CTL3 CTL1 OSL CL 0.7 1 180.00 ! ethyl acetate, 12/92 CTL2 CTL1 OSL CL 0.7 1 180.00 ! ethyl acetate, 12/92 CTL1 CTL2 CL OSL -0.15 1 180.00 ! methyl propionate, 12/92 CTL1 CTL2 CL OSL 0.53 2 180.00 ! methyl propionate, 12/92 CTL2 CTL2 CL OSL -0.15 1 180.00 ! methyl propionate, 12/92 CTL2 CTL2 CL OSL 0.53 2 180.00 ! methyl propionate, 12/92 CTL3 CTL2 CL OSL -0.15 1 180.00 ! methyl propionate, 12/92 CTL3 CTL2 CL OSL 0.53 2 180.00 ! methyl propionate, 12/92 X CTL2 NTL X 0.26 3 0.00 ! tetramethylammonium X CTL5 NTL X 0.23 3 0.00 ! tetramethylammonium X CTL2 NH3L X 0.10 3 0.00 ! ethanolamine NH3L CTL2 CTL2 OHL 0.7 1 180.00 ! ethanolamine NH3L CTL2 CTL2 OSL 0.7 1 180.00 ! ethanolamine NTL CTL2 CTL2 OHL 4.3 1 180.00 ! choline, 12/92 NTL CTL2 CTL2 OHL -0.4 3 180.00 ! choline, 12/92 NTL CTL2 CTL2 OSL 3.3 1 180.00 ! choline, 12/92 NTL CTL2 CTL2 OSL -0.4 3 180.00 ! choline, 12/92 X CTL1 CTL1 X 0.200 3 0.00 ! alkane, 3/92 X CTL1 CTL2 X 0.200 3 0.00 ! alkane, 3/92 X CTL1 CTL3 X 0.200 3 0.00 ! alkane, 3/92 X CTL2 CTL2 X 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell X CTL2 CTL3 X 0.1600 3 0.00 ! alkane, 4/98, yin and mackerell X CTL3 CTL3 X 0.1525 3 0.00 ! alkane, 4/98, yin and mackerell CTL3 CTL2 CTL2 CTL3 0.03178 6 180.00 ! alkane, 4/04, jbk CTL3 CTL2 CTL2 CTL3 0.03819 2 0.00 ! alkane, 4/04, jbk CTL2 CTL2 CTL2 CTL3 0.20391 5 0.00 ! alkane, 4/04, jbk CTL2 CTL2 CTL2 CTL3 0.10824 4 0.00 ! alkane, 4/04, jbk CTL2 CTL2 CTL2 CTL3 0.08133 3 180.00 ! alkane, 4/04, jbk CTL2 CTL2 CTL2 CTL3 0.15051 2 0.00 ! alkane, 4/04, jbk CTL2 CTL2 CTL2 CTL2 0.11251 5 0.00 ! alkane, 4/04, jbk CTL2 CTL2 CTL2 CTL2 0.09458 4 0.00 ! alkane, 4/04, jbk CTL2 CTL2 CTL2 CTL2 0.14975 3 180.00 ! alkane, 4/04, jbk CTL2 CTL2 CTL2 CTL2 0.06450 2 0.00 ! alkane, 4/04, jbk HAL3 CTL3 OSL SL 0.00 3 0.00 ! methylsulfate CTL2 OSL SL O2L 0.00 3 0.00 ! methylsulfate CTL3 OSL SL O2L 0.00 3 0.00 ! methylsulfate HEL1 CEL1 CEL1 HEL1 1.0000 2 180.00 ! 2-butene, adm jr., 8/98 update CTL3 CEL1 CEL1 HEL1 1.0000 2 180.00 ! 2-butene, adm jr., 8/98 update X CEL1 CEL1 X 0.1500 1 0.00 ! 2-butene, adm jr., 2/00 update X CEL1 CEL1 X 8.5000 2 180.00 ! 2-butene, adm jr., 2/00 update X CEL2 CEL2 X 4.9000 2 180.00 ! ethene, yin,adm jr., 12/95 CTL2 CEL1 CEL2 HEL2 5.2000 2 180.00 ! propene, yin,adm jr., 12/95 CTL3 CEL1 CEL2 HEL2 5.2000 2 180.00 ! propene, yin,adm jr., 12/95 HEL1 CEL1 CEL2 HEL2 5.2000 2 180.00 ! propene, yin,adm jr., 12/95 CEL1 CEL1 CTL2 HAL2 0.0300 3 0.00 ! butene, yin,adm jr., 12/95 CEL1 CEL1 CTL3 HAL3 0.0300 3 0.00 ! butene, yin,adm jr., 12/95 CEL1 CEL1 CTL2 CTL2 0.5000 1 180.00 ! 1-butene, adm jr., 2/00 update CEL1 CEL1 CTL2 CTL2 1.3000 3 180.00 ! 1-butene, adm jr., 2/00 update CEL1 CEL1 CTL2 CTL3 0.5000 1 180.00 ! 1-butene, adm jr., 2/00 update CEL1 CEL1 CTL2 CTL3 1.3000 3 180.00 ! 1-butene, adm jr., 2/00 update CEL2 CEL1 CTL2 CTL2 0.5000 1 180.00 ! 1-butene, adm jr., 2/00 update CEL2 CEL1 CTL2 CTL2 1.3000 3 180.00 ! 1-butene, adm jr., 2/00 update CEL2 CEL1 CTL2 CTL3 0.5000 1 180.00 ! 1-butene, adm jr., 2/00 update CEL2 CEL1 CTL2 CTL3 1.3000 3 180.00 ! 1-butene, adm jr., 2/00 update CEL2 CEL1 CTL2 HAL2 0.1200 3 0.00 ! 1-butene, yin,adm jr., 12/95 CEL2 CEL1 CTL3 HAL3 0.0500 3 180.00 ! propene, yin,adm jr., 12/95 HEL1 CEL1 CTL2 CTL2 0.1200 3 0.00 ! butene, yin,adm jr., 12/95 HEL1 CEL1 CTL2 CTL3 0.1200 3 0.00 ! butene, yin,adm jr., 12/95 HEL1 CEL1 CTL2 HAL2 0.0000 3 0.00 ! butene, adm jr., 2/00 update HEL1 CEL1 CTL3 HAL3 0.0000 3 0.00 ! butene, adm jr., 2/00 update ! 1,4-dipentene, adm jr., 2/00 CEL2 CEL1 CTL2 CEL1 1.200 1 180.00 !1,4-dipentene CEL2 CEL1 CTL2 CEL1 0.400 2 180.00 !1,4-dipentene CEL2 CEL1 CTL2 CEL1 1.300 3 180.00 !1,4-dipentene CEL1 CTL2 CEL1 HEL1 0.000 2 0.00 !1,4-dipentene CEL1 CTL2 CEL1 HEL1 0.000 3 0.00 !1,4-dipentene ! 2,5-diheptene, adm jr., 2/00 ! for CIS double bonds in polyunsaturated lipids (default) CEL1 CEL1 CTL2 CEL1 1.000 1 180.00 !2,5-diheptane CEL1 CEL1 CTL2 CEL1 0.100 2 0.00 !2,5-diheptane CEL1 CEL1 CTL2 CEL1 0.300 3 180.00 !2,5-diheptane CEL1 CEL1 CTL2 CEL1 0.200 4 0.00 !2,5-diheptane ! for TRANS double bonds in polyunsaturated lipids ! uncomment following 4 lines and comment previous 4 lines to use !CEL1 CEL1 CTL2 CEL1 1.200 1 180.00 !2,5-diheptane !CEL1 CEL1 CTL2 CEL1 0.200 2 180.00 !2,5-diheptane !CEL1 CEL1 CTL2 CEL1 1.200 3 180.00 !2,5-diheptane !CEL1 CEL1 CTL2 CEL1 0.100 4 180.00 !2,5-diheptane IMPROPER ! !V(improper) = Kpsi(psi - psi0)**2 ! !Kpsi: kcal/mole/rad**2 !psi0: degrees !note that the second column of numbers (0) is ignored ! !atom types Kpsi psi0 ! OBL X X CL 100.00 0 0.00 ! acetic acid HEL2 HEL2 CEL2 CEL2 3.00 0 0.00 ! ethene, yin,adm jr., 12/95 OCL X X CL 96.00 0 0.00 ! acetate NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch - cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 ! !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] ! !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j ! !atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 ! HOL 0.0 -0.046 0.2245 HAL1 0.0 -0.022 1.3200 ! alkane, 3/92 HAL2 0.0 -0.028 1.3400 ! alkane, yin and mackerell, 4/98 HAL3 0.0 -0.024 1.3400 ! alkane, yin and mackerell, 4/98 HCL 0.0 -0.046 0.2245 ! ethanolamine HT 0.0 -0.046 0.2245 HL 0.0 -0.046 0.7 ! polar H on NC4+ HEL1 0.0 -0.031 1.25 ! alkene, yin,adm jr., 12/95 HEL2 0.0 -0.026 1.26 ! alkene, yin,adm jr., 12/95 ! CL 0.0 -0.070 2.00 ! methyl acetate update CTL1 0.0 -0.0200 2.275 0.0 -0.01 1.9 ! alkane, 3/92 CTL2 0.0 -0.0560 2.010 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr. CTL3 0.0 -0.0780 2.040 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr. CTL5 0.0 -0.0800 2.06 0.0 -0.01 1.9 ! old CTL3 ! maintained for tetramethylammonium CEL1 0.0 -0.068 2.09 ! alkene, yin,adm jr., 12/95 CEL2 0.0 -0.064 2.08 ! alkene, yin,adm jr., 12/95 ! OBL 0.0 -0.12 1.70 0.0 -0.12 1.4 OCL 0.0 -0.12 1.70 O2L 0.0 -0.12 1.70 OHL 0.0 -0.1521 1.77 OSL 0.0 -0.1521 1.77 OT 0.0 -0.1521 1.7682 ! NH3L 0.0 -0.20 1.85 ! ethanolamine NTL 0.0 -0.20 1.85 ! as all other nitogens ! SL 0.0 -0.47 2.1 ! methylsulfate PL 0.0 -0.585 2.15 ! ADM Jr. DUM 0.0 -0.00 0.0 ! dummy atom ! ! ions, note lack of NBFIXes ! SOD 0.0 -0.0469 1.36375 ! sodium ! D. Beglovd and B. Roux, dA=-100.8 kcal/mol POT 0.0 -0.0870 1.76375 ! potassium ! D. Beglovd and B. Roux, dA=-82.36+2.8 = -79.56 kca/mol CLA 0.0 -0.150 2.27 ! chloride ! D. Beglovd and B. Roux, dA=-83.87+4.46 = -79.40 kcal/mol MG 0.0 -0.0150 1.18500 ! Magnesium ! B. Roux dA = -441.65 NBFIX ! Emin Rmin ! (kcal/mol) (A) ! HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use ! READ PARAM APPEND CARD ! to append hbond parameters from the file: par_hbond.inp END