* \\\\\\\ CHARMM27rn All-Hydrogen Nitro Parameter File /////// * \\\\\\\\\\\\\\\\\\ Developmental ///////////////////////// * Jeffery B. Klauda * September 2007 * All comments to JBK email:jbklauda,umd.edu * !references ! BONDS ! !V(bond) = Kb(b - b0)**2 ! !Kb: kcal/mole/A**2 !b0: A ! !atom type Kb b0 ! 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 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 HT HT 0.0 1.5139 ! from TIPS3P geometry (for SHAKE w/PARAM) HT OT 450.0 0.9572 ! from TIPS3P geometry NO ON 550.0 1.225 ! Nitro, OPLS-AA CTL2 NO 375.0 1.490 ! Nitro, OPLS-AA CTL3 NO 375.0 1.490 ! Nitro, OPLS-AA CG2R61 NG2O1 230.00 1.4020 ! NITB, nitrobenzene NG2O1 OG2N1 580.00 1.2250 ! NITB, nitrobenzene CG2R61 CG2R61 305.000 1.3750 ! ALLOW ARO ! benzene, JES 8/25/89 HGR61 CG2R61 340.000 1.0830 ! ALLOW ARO ! trp, adm jr., 10/02/89 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 ! 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 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 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 CTL3 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 HT OT HT 55.0 104.52 ! FROM TIPS3P GEOMETRY CTL2 NO ON 80.0 117.5 ! Nitro, OPLS-AA CTL3 NO ON 80.0 117.5 ! Nitro, OPLS-AA CTL2 CTL2 NO 63.0 111.1 ! Nitro, OPLS-AA CTL3 CTL2 NO 63.0 111.1 ! Nitro, OPLS-AA HAL2 CTL2 NO 35.0 105.0 ! Nitro, OPLS-AA HAL3 CTL3 NO 35.0 105.0 ! Nitro, OPLS-AA ON NO ON 80.0 125.0 ! Nitro, OPLS-AA CG2R61 CG2R61 NG2O1 20.00 120.00 ! NITB, nitrobenzene CG2R61 NG2O1 OG2N1 65.00 116.00 ! NITB, nitrobenzene OG2N1 NG2O1 OG2N1 105.00 128.00 ! NITB, nitrobenzene CG2R61 CG2R61 CG2R61 40.000 120.00 35.00 2.41620 ! ALLOW ARO ! JES 8/25/89 HGR61 CG2R61 CG2R61 29.000 120.00 25.00 2.15250 ! ALLOW ARO ! trp, adm jr., 10/02/89 DIHEDRALS ! !V(dihedral) = Kchi(1 + cos(n(chi) - delta)) ! !Kchi: kcal/mole !n: multiplicity !delta: degrees ! !atom types Kchi n delta ! 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 HAL2 CTL2 CTL2 NO 0.000 3 180.00 ! Nitro, 5/07, jbk HAL3 CTL3 CTL2 NO 0.000 3 180.00 ! Nitro, 5/07, jbk HAL2 CTL2 NO ON 0.000 1 0.00 ! Nitro, 5/07, jbk HAL3 CTL3 NO ON 0.000 1 0.00 ! Nitro, 5/07, jbk CTL2 CTL2 NO ON 0.060 2 0.00 ! Nitro, 5/07, jbk CTL3 CTL2 NO ON 0.000 3 0.00 ! Nitro, 5/07, jbk CTL3 CTL2 CTL2 NO 0.084 4 0.00 ! Nitro, 5/07, jbk CTL3 CTL2 CTL2 NO 0.360 3 0.00 ! Nitro, 5/07, jbk CTL3 CTL2 CTL2 NO 0.151 2 0.00 ! Nitro, 5/07, jbk CTL3 CTL2 CTL2 NO 0.133 1 180.00 ! Nitro, 5/07, jbk CTL2 CTL2 CTL2 NO 0.084 4 0.00 ! Nitro, 5/07, jbk CTL2 CTL2 CTL2 NO 0.360 3 0.00 ! Nitro, 5/07, jbk CTL2 CTL2 CTL2 NO 0.151 2 0.00 ! Nitro, 5/07, jbk CTL2 CTL2 CTL2 NO 0.133 1 180.00 ! Nitro, 5/07, jbk CG2R61 CG2R61 CG2R61 NG2O1 6.1400 2 180.00 ! NITB, nitrobenzene NG2O1 CG2R61 CG2R61 HGR61 1.0000 2 180.00 ! NITB, nitrobenzene CG2R61 CG2R61 NG2O1 OG2N1 1.1000 2 180.00 ! NITB, nitrobenzene CG2R61 CG2R61 CG2R61 CG2R61 3.1000 2 180.00 ! ALLOW ARO ! JES 8/25/89 HGR61 CG2R61 CG2R61 CG2R61 3.5000 2 180.00 ! ALLOW ARO ! adm jr., 10/02/89 HGR61 CG2R61 CG2R61 HGR61 2.5000 2 180.00 ! ALLOW ARO ! ADM JR., 10/02/89 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 ! HEL2 HEL2 CEL2 CEL2 3.00 0 0.00 ! ethene, yin,adm jr., 12/95 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 OSP 0.0 -0.1521 1.77 OT 0.0 -0.1521 1.7682 ON 0.0 -0.1200 1.7000 ! ADM, Jr, Nitrobenzene ! NH3L 0.0 -0.20 1.85 ! ethanolamine NTL 0.0 -0.20 1.85 ! as all other nitogens NO 0.0 -0.1600 1.837 ! jbk, OPLS/NB-alex average ! 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 NG2O1 0.0 -0.1200 1.8500 ! jbk, 7/07 OG2N1 0.0 -0.1000 1.7700 ! jbk, 7/07 CG2R61 0.000000 -0.070000 1.992400 ! benzene (JES) HGR61 0.0 -0.046 1.1000 !adm jr. aromatic Hvdw 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