*>>>>>>>>>>>>>>>>> All-hydrogen parameters <<<<<<<<<<<<<<<<<<<<<<< *>>>>>>>>>>>>>>>> CHARMM32 ether force field <<<<<<<<<<<<<<<<<<<<< *>>>>>>>>>>>>>>>>>>>>>> December 2006 <<<<<<<<<<<<<<<<<<<<<<<<<<<< *>>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<< *>>>>>>>>>>>> via the CHARMM forum: www.charmm.org <<<<<<<<<<<<<<< * !Vorobyov, I., Anisimov, V.M., Greene, S., Venable, R.M., Moser, A., !Pastor, R.W., and MacKerell, A.D., Jr. "Additive and Classical Drude !Polarizable Force Fields for Linear and Cyclic Ethers," Journal of !Chemical Theory and Computing, 3: 1120-1133, 2007 ! ! O-C-C-O torsion modified; HK Lee, RM Venable, RW Pastor August 2007 ! ! Hwankyu Lee, Richard M Venable, Alexander D MacKerell Jr., Richard W Pastor ! Molecular dynamics studies of polyethylene oxide and polyethylene glycol: ! Hydrodynamic radius and shape anisotropy ! Biophysical J., in press (2008) ! ! ********* V(bond) = Kb(b - b0)**2 BONDS !! Alkane standard C27 parameeters. Not modified from original. CC31A HCA1 309.00 1.111 ! alkanes, 4/98 CC32A HCA2 309.00 1.111 ! alkanes, 4/98 CC33A HCA3 322.00 1.111 ! alkanes, 4/98 CC30A CC32A 222.50 1.538 ! 10/98 CC30A CC33A 222.50 1.538 ! 10/98 CC31A CC31A 222.50 1.500 ! alkanes, 3/92 CC31A CC32A 222.50 1.538 ! alkanes, 3/92 CC31A CC33A 222.50 1.538 ! alkanes, 3/92 CC32A CC32A 222.50 1.530 ! alkanes, 3/92 CC32A CC33A 222.50 1.528 ! alkanes, 3/92 CC33A CC33A 222.50 1.530 ! alkanes, 3/92 CC325A CC325A 195.00 1.548 ! cyclopentane CPEN 10/17/05 viv CC325A HCA25A 307.00 1.116 ! cyclopentane CPEN 10/17/05 viv CC325B OC305A 350.00 1.425 ! THF, nucleotide CSD/NDB survey, 5/30/06,viv CC325B CC325B 195.00 1.518 ! THF, nucleotide CSD/NDB survey, 5/30/06,viv CC325B HCA25A 307.00 1.100 ! THF, THF neutron diffr., 5/30/06, viv CC325B CC33A 222.50 1.528 ! TF2M, viv CC32A OC30A 360.00 1.415 ! DEET, diethylether, alex CC33A OC30A 360.00 1.415 ! DEET, diethylether, alex CC326A HCA2 309.00 1.111 ! THP, viv CC326A CC326A 222.50 1.530 ! THP, viv CC326A OC30A 360.00 1.415 ! DEET, diethylether, viv !! Original TIP3P water parameters HT HT 0.00 1.5139 ! TIPS3P GEOMETRY (FOR SHAKE/W PARAM) OT HT 450.00 0.9572 ! TIPS3P GEOMETRY ! ********* V(angle) = Ktheta(Theta - Theta0)**2 ANGLES !! Alkane standard C27 parameeters. Not modified from original. HCA1 CC31A CC31A 34.500 110.10 22.53 2.179 ! alkane, 3/92 HCA1 CC31A CC32A 34.500 110.10 22.53 2.179 ! alkane, 3/92 HCA1 CC31A CC33A 34.500 110.10 22.53 2.179 ! alkane, 3/92 HCA2 CC32A CC30A 26.500 110.10 22.53 2.179 ! alkane, 4/98 HCA2 CC32A CC31A 26.500 110.10 22.53 2.179 ! alkane, 4/98 HCA2 CC32A CC32A 26.500 110.10 22.53 2.179 ! alkane, 4/98 HCA2 CC32A CC33A 34.600 110.10 22.53 2.179 ! alkane, 4/98 HCA3 CC33A CC30A 33.430 110.10 22.53 2.179 ! alkane, 4/98 HCA3 CC33A CC31A 33.430 110.10 22.53 2.179 ! alkane, 4/98 HCA3 CC33A CC32A 34.600 110.10 22.53 2.179 ! alkane, 4/98 HCA3 CC33A CC33A 37.500 110.10 22.53 2.179 ! alkane, 4/98 HCA2 CC32A HCA2 35.50 109.00 5.40 1.802 ! alkane, 3/92 HCA3 CC33A HCA3 35.50 108.40 5.40 1.802 ! alkane, 3/92 CC30A CC32A CC32A 58.350 113.50 11.16 2.561 ! glycerol CC30A CC32A CC33A 58.350 113.50 11.16 2.561 ! glycerol CC31A CC31A CC31A 53.350 111.00 8.00 2.561 ! alkane, 3/92 CC31A CC31A CC32A 58.350 113.50 11.16 2.561 ! glycerol CC31A CC31A CC33A 53.350 108.50 8.00 2.561 ! alkane, 3/92 CC31A CC32A CC31A 58.350 113.50 11.16 2.561 ! glycerol CC31A CC32A CC32A 58.350 113.50 11.16 2.561 ! glycerol CC31A CC32A CC33A 58.350 113.50 11.16 2.561 ! glycerol CC32A CC30A CC32A 58.350 113.50 11.16 2.561 ! glycerol CC32A CC31A CC32A 58.350 113.50 11.16 2.561 ! glycerol CC32A CC32A CC32A 58.350 113.60 11.16 2.561 ! alkane, 3/92 CC32A CC32A CC33A 58.000 115.00 8.00 2.561 ! alkane, 3/92 CC33A CC30A CC33A 53.350 114.00 8.00 2.561 ! alkane 3/2/92 CC33A CC31A CC32A 53.350 114.00 8.00 2.561 ! alkane 3/2/92 CC33A CC31A CC33A 53.350 114.00 8.00 2.561 ! alkane 3/2/92 CC33A CC32A CC33A 53.350 114.00 8.00 2.561 ! alkane 3/2/92 !! 5-membered ring cyclopentane (cpen) ring parameters. viv modified Oct. 05 CC325A CC325A CC325A 58.00 106.00 11.16 2.561 ! CPEN 10/17/05 viv HCA25A CC325A CC325A 35.00 111.40 22.53 2.179 ! CPEN 10/17/05 viv HCA25A CC325A HCA25A 38.50 106.80 5.40 1.802 ! CPEN 10/17/05 viv HCA25A CC325B CC325B 35.00 111.40 22.53 2.179 ! TF2M, viv HCA25A CC325B HCA25A 38.50 106.80 5.40 1.802 ! THF, 10/17/05 viv CC325B CC325B CC325B 58.00 109.50 11.16 2.561 ! THF, nucleotide CSD/NDB survey, 05/30/06, viv OC305A CC325B CC325B 45.00 111.10 ! THF 10/21/05, viv CC325B OC305A CC325B 95.00 111.00 ! THF 10/21/05, viv HCA25A CC325B OC305A 70.00 107.30 ! THF 10/21/05, viv HCA3 CC33A CC325B 34.600 110.10 22.53 2.179 ! TF2M viv CC325B CC325B CC33A 58.000 115.00 8.00 2.561 ! TF2M viv HCA25A CC325B CC33A 34.600 110.10 22.53 2.179 ! TF2M viv OC305A CC325B CC33A 45.00 111.50 ! TF2M, viv CC32A OC30A CC32A 95.00 109.70 ! DEET, diethylether, alex CC33A OC30A CC32A 95.00 109.70 ! DEET, diethylether, alex CC33A OC30A CC33A 95.00 109.70 ! DEET, diethylether, alex OC30A CC32A CC32A 45.00 111.50 ! DEET, diethylether, alex OC30A CC32A CC33A 45.00 111.50 ! DEET, diethylether, alex HCA3 CC33A OC30A 60.00 109.50 ! phosphate, alex HCA2 CC32A OC30A 60.00 109.50 ! phosphate, alex HCA2 CC326A CC326A 34.500 110.10 22.53 2.179 ! THP, sng cyclohexane 12/05 HCA2 CC326A HCA2 35.50 109.00 5.40 1.80200! THP, viv CC326A CC326A CC326A 58.350 112.00 11.16 2.561 ! THP, sng cyclohexane 12/05 OC30A CC326A CC326A 45.00 111.50 ! THP, viv CC326A OC30A CC326A 95.00 109.70 ! THP, viv HCA2 CC326A OC30A 45.00 109.50 ! THP, sng 02/06 HT OT HT 55.00 104.52 ! TIP3P GEOMETRY ! ******** V(dihedral) = Kchi(1 + cos(n(chi) - delta)) DIHEDRALS !! Alkane standard C27 parameters. Not modified from original. CC31A CC30A CC32A HCA2 0.20000 3 0.00 ! alkane, 3/92 CC32A CC30A CC32A HCA2 0.20000 3 0.00 ! alkane, 3/92 CC33A CC30A CC32A HCA2 0.20000 3 0.00 ! alkane, 3/92 CC31A CC30A CC33A HCA3 0.20000 3 0.00 ! alkane, 3/92 CC32A CC30A CC32A HCA3 0.20000 3 0.00 ! alkane, 3/92 CC33A CC30A CC32A HCA3 0.20000 3 0.00 ! alkane, 3/92 HCA1 CC31A CC31A HCA1 0.20000 3 0.00 ! alkane, 3/92 CC31A CC31A CC31A HCA1 0.20000 3 0.00 ! alkane, 3/92 CC32A CC31A CC31A HCA1 0.20000 3 0.00 ! alkane, 3/92 CC33A CC31A CC31A HCA1 0.20000 3 0.00 ! alkane, 3/92 HCA1 CC31A CC32A HCA2 0.20000 3 0.00 ! alkane, 3/92 HCA1 CC31A CC32A CC31A 0.20000 3 0.00 ! alkane, 3/92 HCA1 CC31A CC32A CC32A 0.20000 3 0.00 ! alkane, 3/92 HCA1 CC31A CC32A CC33A 0.20000 3 0.00 ! alkane, 3/92 CC31A CC31A CC32A HCA2 0.20000 3 0.00 ! alkane, 3/92 CC32A CC31A CC32A HCA2 0.20000 3 0.00 ! alkane, 3/92 CC33A CC31A CC32A HCA2 0.20000 3 0.00 ! alkane, 3/92 HCA1 CC31A CC33A HCA3 0.20000 3 0.00 ! alkane, 3/92 CC31A CC31A CC33A HCA3 0.20000 3 0.00 ! alkane, 3/92 CC32A CC31A CC33A HCA3 0.20000 3 0.00 ! alkane, 3/92 CC33A CC31A CC33A HCA3 0.20000 3 0.00 ! alkane, 3/92 HCA2 CC32A CC32A HCA2 0.19000 3 0.0 ! alkane, 4/98, yin and mackerell CC30A CC32A CC32A HCA2 0.19000 3 0.00 ! alkane, 4/98, yin and mackerell CC31A CC32A CC32A HCA2 0.19000 3 0.00 ! alkane, 4/98, yin and mackerell CC32A CC32A CC32A HCA2 0.19000 3 0.00 ! alkane, 4/98, yin and mackerell CC33A CC32A CC32A HCA2 0.19000 3 0.00 ! alkane, 4/98, yin and mackerell HCA2 CC32A CC33A HCA3 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell CC30A CC32A CC33A HCA3 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell CC31A CC32A CC33A HCA3 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell CC32A CC32A CC33A HCA3 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell CC33A CC32A CC33A HCA3 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell CC33A CC32A CC32A CC33A 0.03179 6 180.0 ! alkane, c27r klauda et al 2004 CC33A CC32A CC32A CC33A 0.03819 2 0.0 ! alkane, c27r klauda et al 2004 CC33A CC32A CC32A CC32A 0.20391 5 0.0 ! alkane, c27r klauda et al 2004 CC33A CC32A CC32A CC32A 0.10824 4 0.0 ! alkane, c27r klauda et al 2004 CC33A CC32A CC32A CC32A 0.08133 3 180.0 ! alkane, c27r klauda et al 2004 CC33A CC32A CC32A CC32A 0.15051 2 0.0 ! alkane, c27r klauda et al 2004 CC32A CC32A CC32A CC32A 0.11251 5 0.0 ! alkane, c27r klauda et al 2004 CC32A CC32A CC32A CC32A 0.09458 4 0.0 ! alkane, c27r klauda et al.2004 CC32A CC32A CC32A CC32A 0.14975 3 180.0 ! alkane, c27r klauda et al 2004 CC32A CC32A CC32A CC32A 0.06450 2 0.0 ! alkane, c27r klauda et al 2004 CC33A CC325A CC325A CC33A 0.16000 3 0.0 !alkane, 4/98, yin and mackerell, cpen, viv CC33A CC325A CC325A CC325A 0.16000 3 0.0 !alkane, 4/98, yin and mackerell, cpen, viv CC33A CC325A CC325A HCA25A 0.16000 3 0.0 !alkane, 4/98, yin and mackerell, cpen, viv HCA25A CC325A CC325A HCA25A 0.16000 3 0.0 !alkane, 4/98, yin and mackerell, cpen, viv CC325A CC325A CC325A HCA25A 0.16000 3 0.0 !alkane, 4/98, yin and mackerell, cpen, viv CC325A CC325A CC325A CC325A 0.41000 3 180.0 ! cpen, cyclopentane, viv 10/4/05 CC33A CC325B CC325B CC33A 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thf, viv CC33A CC325B CC325B CC325B 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thf, viv CC33A CC325B CC325B HCA25A 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thf, viv HCA25A CC325B CC325B HCA25A 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thf, viv CC325B CC325B CC325B HCA25A 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thf, viv OC305A CC325B CC325B HCA25A 0.19000 3 0.0 ! alkane, 4/98, yin and mackerell, thf viv HCA25A CC325B CC33A HCA3 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell, tf2m viv CC325B CC325B CC33A HCA3 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell, tf2m viv OC305A CC325B CC33A HCA3 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell, tf2m viv CC325B CC325B CC325B CC325B 0.41000 3 180.0 ! CPEN viv 10/4/05 HCA25A CC325B OC305A CC325B 0.3000 3 0.0 ! THF, 05/30/06, viv OC305A CC325B CC325B CC325B 0.0000 3 0.0 ! THF, 05/30/06, viv CC325B CC325B OC305A CC325B 0.5000 3 0.0 ! THF, 05/30/06, viv CC33A CC325B OC305A CC325B 0.3000 3 0.0 ! THF, 05/30/06, viv OC305A CC325B CC325B OC305A 0.59 1 180.0 ! 1,2 dimethoxyethane, Aug 2007, HK Lee GUESS!!!!!!!!!!! OC305A CC325B CC325B OC305A 1.16 2 0.0 ! 1,2 dimethoxyethane GUESS!!!!!!!!!!! CC33A CC326A CC326A CC33A 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thp, viv CC33A CC326A CC326A CC326A 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thp, viv CC33A CC326A CC326A HCA2 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thp, viv HCA2 CC326A CC326A HCA2 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thp, viv HCA2 CC326A CC326A CC326A 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thp, viv OC30A CC326A CC326A HCA2 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thp viv HCA2 CC326A CC33A HCA3 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell, me-thp viv CC326A CC326A CC33A HCA3 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell, me-thp viv OC30A CC326A CC33A HCA3 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell, me-thp viv CC326A CC326A CC326A CC326A 0.49829 2 0.0 ! THP, viv CC326A CC326A CC326A CC326A -0.59844 3 0.0 ! THP, viv CC326A CC326A CC326A CC326A 0.41746 4 0.0 ! THP, viv CC326A CC326A CC326A CC326A -0.24829 5 0.0 ! THP, viv OC30A CC326A CC326A CC326A -0.19225 1 0.0 ! THP, sng 1/06 OC30A CC326A CC326A CC326A -1.00000 2 0.0 ! THP, sng 1/06 OC30A CC326A CC326A CC326A 0.59457 3 0.0 ! THP, sng 1/06 OC30A CC326A CC326A CC326A -0.07862 4 0.0 ! THP, sng 1/06 HCA3 CC33A CC33A HCA3 0.15250 3 0.00 ! ETHA, ethane, 4/98, yin and mackerell CC326A OC30A CC326A CC326A -0.52702 1 0.0 ! THP, sng 1/06 CC326A OC30A CC326A CC326A 0.68297 2 0.0 ! THP, sng 1/06 CC326A OC30A CC326A CC326A -0.20977 3 0.0 ! THP, sng 1/06 CC326A OC30A CC326A CC326A 0.15037 4 0.0 ! THP, sng 1/06 CC326A OC30A CC326A HCA2 0.28400 3 0.0 ! DMET, viv HCA2 CC32A CC32A OC30A 0.19000 3 0.0 ! alkane, 4/98, yin and mackerell OC30A CC32A CC33A HCA3 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell HCA2 CC32A OC30A CC32A 0.28400 3 0.0 ! DEET, diethylether, alex HCA3 CC33A OC30A CC32A 0.28400 3 0.0 ! DEET, diethylether, alex HCA2 CC32A OC30A CC33A 0.28400 3 0.0 ! DEET, diethylether, alex HCA3 CC33A OC30A CC33A 0.28400 3 0.0 ! DME, viv CC33A CC32A OC30A CC32A 0.40 1 0.0 ! diethylether, 2/12/05, ATM CC33A CC32A OC30A CC32A 0.49 3 0.0 ! diethylether CC33A CC32A OC30A CC33A 0.40 1 0.0 ! diethylether, 2/12/05, ATM, MEE viv CC33A CC32A OC30A CC33A 0.49 3 0.0 ! diethylether, MEE viv CC32A CC32A OC30A CC33A 0.57 1 0.0 ! 1,2 dimethoxyethane (DME), 2/12/05, ATM CC32A CC32A OC30A CC33A 0.29 2 0.0 ! 1,2 dimethoxyethane (DME) CC32A CC32A OC30A CC33A 0.43 3 0.0 ! 1,2 dimethoxyethane (DME) CC32A CC32A OC30A CC32A 0.57 1 0.0 ! 1,2 dimethoxyethane, 2/12/05, ATM CC32A CC32A OC30A CC32A 0.29 2 0.0 ! 1,2 dimethoxyethane CC32A CC32A OC30A CC32A 0.43 3 0.0 ! 1,2 dimethoxyethane OC30A CC32A CC32A OC30A 0.59 1 180.0 ! 1,2 dimethoxyethane, Aug 2007, HK Lee OC30A CC32A CC32A OC30A 1.16 2 0.0 ! 1,2 dimethoxyethane OC30A CC32A CC32A CC33A 0.16 1 180.0 ! methylpropylether, 2/12/05, ATM OC30A CC32A CC32A CC33A 0.39 2 0.0 ! methylpropylether OC30A CC32A CC32A CC32A 0.16 1 180.0 ! methylpropylether, 2/12/05, ATM OC30A CC32A CC32A CC32A 0.39 2 0.0 ! methylpropylether !********* V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] 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 HCA1 0.0 -0.0450 1.3400 ! alkane,isobutane 1/5/05 viv HCA2 0.0 -0.0350 1.3400 ! alkane,propane 11/16/04 viv HCA3 0.0 -0.0240 1.3400 ! alkane, yin and mackerell, 4/98 HT 0.0 -0.0460 0.2245 ! TIP3P water CC30A 0.0 -0.0320 2.0000 0.0 -0.01 1.9 ! from CC31A CC31A 0.0 -0.0320 2.0000 0.0 -0.01 1.9 ! alkane,isobutane 1/5/05 viv CC32A 0.0 -0.0560 2.0100 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr. CC33A 0.0 -0.0780 2.0400 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr. CC326A 0.0 -0.0560 2.0100 0.0 -0.01 1.9 ! THP, tetrahyropyran, viv HCA25A 0.0 -0.0350 1.3000 ! CPEN, cyclopentane, 8/06 viv CC325A 0.0 -0.0600 2.0200 0.0 -0.01 1.9 ! CPEN, cyclopentane, 8/06 viv CC325B 0.0 -0.0600 2.0200 0.0 -0.01 1.9 ! CPEN, cyclopentane, 8/06 viv OC305A 0.0 -0.1000 1.6500 ! THP, tetrahydropyran sng 1/06 OC30A 0.0 -0.1000 1.6500 ! THP, tetrahydropyran sng 1/06 OT 0.0 -0.1521 1.7682 ! TIP3P water ! HE 0.0 -0.021270 1.4800 ! helium, experimental pot. energy surface, adm jr., 12/95 NE 0.0 -0.086000 1.5300 ! neon, semiempirical pot. energy surface, adm jr., 12/95 ! ions and miscellaneous types SOD 0.0 -0.0469 1.36375 ! sodium POT 0.0 -0.0870 1.76375 ! potassium ! D. Beglovd and B. Roux, dA=-100.8 kcal/mol DUM 0.0 -0.0000 0.0000 ! dummy atom END