Commit 28b22a9b authored by NOEL Philippe's avatar NOEL Philippe

Solve conflict in tools.rs

parents 8f248f06 5cf4f49b
Pipeline #75844 passed with stages
in 2 minutes and 52 seconds
[package]
name = "pdbparser"
version = "1.0.0"
authors = ["NOEL Philippe <philippe.noel@inria.fr>"]
authors = ["NOEL Philippe <philippe.noel@inria.fr>", "BRESSO Emmanuel <emmanuel.bresso@loria.fr>"]
edition = "2018"
include = ["Cargo.toml", "src/**/*.rs", "tests/**/*.rs", "README.md"]
......
*>>>>>>>>>>>>>>>>> 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., 95: 1590-1599, 2008
!
! ********* V(bond) = Kb(b - b0)**2
ATOMS
MASS -1 HCA1A 1.00800 ! Alkane H attached to C(sp3)H (eq. HA1)
MASS -1 HCA2A 1.00800 ! Alkane H attached to C(sp3)H2 (eq. HA2)
MASS -1 HCA3A 1.00800 ! Alkane H attached to C(sp3)H3 (eq. HA3)
MASS -1 HCA25A 1.00800 ! Alkane H attached to C(sp3)H2 in 5-membered ring
MASS -1 CC30A 12.01100 ! -C(sp3) Carbon (eq. CT)
MASS -1 CC31A 12.01100 ! -C(sp3)H Carbon (eq. CT1)
MASS -1 CC32A 12.01100 ! -C(sp3)H2 Carbon (eq. CT2)
MASS -1 CC33A 12.01100 ! -C(sp3)H3 Carbon (eq. CT3)
MASS -1 CC325A 12.01100 ! -C(sp3)H2 Carbon in 5-membered ring
MASS -1 CC325B 12.01100 ! -C(sp3)H2 Carbon in THF (tetrahydrofuran)
MASS -1 CC326A 12.01100 ! -C(sp3)H2 Carbon in THP (tetrahydropyran)
MASS -1 OC30A 15.99940 ! Ether Oxygen
MASS -1 OC305A 15.99940 ! Ether Oxygen in THF
BONDS
!! Alkane standard C27 parameeters. Not modified from original.
CC31A HCA1A 309.00 1.111 ! alkanes, 4/98
CC32A HCA2A 309.00 1.111 ! alkanes, 4/98
CC33A HCA3A 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 HCA2A 309.00 1.111 ! THP, viv
CC326A CC326A 222.50 1.530 ! THP, viv
CC326A OC30A 360.00 1.415 ! DEET, diethylether, viv
! ********* V(angle) = Ktheta(Theta - Theta0)**2
ANGLES
!! Alkane standard C27 parameeters. Not modified from original.
HCA1A CC31A CC31A 34.500 110.10 22.53 2.179 ! alkane, 3/92
HCA1A CC31A CC32A 34.500 110.10 22.53 2.179 ! alkane, 3/92
HCA1A CC31A CC33A 34.500 110.10 22.53 2.179 ! alkane, 3/92
HCA2A CC32A CC30A 26.500 110.10 22.53 2.179 ! alkane, 4/98
HCA2A CC32A CC31A 26.500 110.10 22.53 2.179 ! alkane, 4/98
HCA2A CC32A CC32A 26.500 110.10 22.53 2.179 ! alkane, 4/98
HCA2A CC32A CC33A 34.600 110.10 22.53 2.179 ! alkane, 4/98
HCA3A CC33A CC30A 33.430 110.10 22.53 2.179 ! alkane, 4/98
HCA3A CC33A CC31A 33.430 110.10 22.53 2.179 ! alkane, 4/98
HCA3A CC33A CC32A 34.600 110.10 22.53 2.179 ! alkane, 4/98
HCA3A CC33A CC33A 37.500 110.10 22.53 2.179 ! alkane, 4/98
HCA2A CC32A HCA2A 35.50 109.00 5.40 1.802 ! alkane, 3/92
HCA3A CC33A HCA3A 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
HCA3A 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
HCA3A CC33A OC30A 60.00 109.50 ! phosphate, alex
HCA2A CC32A OC30A 60.00 109.50 ! phosphate, alex
HCA2A CC326A CC326A 34.500 110.10 22.53 2.179 ! THP, sng cyclohexane 12/05
HCA2A CC326A HCA2A 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
HCA2A CC326A OC30A 45.00 109.50 ! THP, sng 02/06
! ******** V(dihedral) = Kchi(1 + cos(n(chi) - delta))
DIHEDRALS
!! Alkane standard C27 parameters. Not modified from original.
CC31A CC30A CC32A HCA2A 0.20000 3 0.00 ! alkane, 3/92
CC32A CC30A CC32A HCA2A 0.20000 3 0.00 ! alkane, 3/92
CC33A CC30A CC32A HCA2A 0.20000 3 0.00 ! alkane, 3/92
CC31A CC30A CC33A HCA3A 0.20000 3 0.00 ! alkane, 3/92
CC32A CC30A CC32A HCA3A 0.20000 3 0.00 ! alkane, 3/92
CC33A CC30A CC32A HCA3A 0.20000 3 0.00 ! alkane, 3/92
HCA1A CC31A CC31A HCA1A 0.20000 3 0.00 ! alkane, 3/92
CC31A CC31A CC31A HCA1A 0.20000 3 0.00 ! alkane, 3/92
CC32A CC31A CC31A HCA1A 0.20000 3 0.00 ! alkane, 3/92
CC33A CC31A CC31A HCA1A 0.20000 3 0.00 ! alkane, 3/92
HCA1A CC31A CC32A HCA2A 0.20000 3 0.00 ! alkane, 3/92
HCA1A CC31A CC32A CC31A 0.20000 3 0.00 ! alkane, 3/92
HCA1A CC31A CC32A CC32A 0.20000 3 0.00 ! alkane, 3/92
HCA1A CC31A CC32A CC33A 0.20000 3 0.00 ! alkane, 3/92
CC31A CC31A CC32A HCA2A 0.20000 3 0.00 ! alkane, 3/92
CC32A CC31A CC32A HCA2A 0.20000 3 0.00 ! alkane, 3/92
CC33A CC31A CC32A HCA2A 0.20000 3 0.00 ! alkane, 3/92
HCA1A CC31A CC33A HCA3A 0.20000 3 0.00 ! alkane, 3/92
CC31A CC31A CC33A HCA3A 0.20000 3 0.00 ! alkane, 3/92
CC32A CC31A CC33A HCA3A 0.20000 3 0.00 ! alkane, 3/92
CC33A CC31A CC33A HCA3A 0.20000 3 0.00 ! alkane, 3/92
HCA2A CC32A CC32A HCA2A 0.19000 3 0.0 ! alkane, 4/98, yin and mackerell
CC30A CC32A CC32A HCA2A 0.19000 3 0.00 ! alkane, 4/98, yin and mackerell
CC31A CC32A CC32A HCA2A 0.19000 3 0.00 ! alkane, 4/98, yin and mackerell
CC32A CC32A CC32A HCA2A 0.19000 3 0.00 ! alkane, 4/98, yin and mackerell
CC33A CC32A CC32A HCA2A 0.19000 3 0.00 ! alkane, 4/98, yin and mackerell
HCA2A CC32A CC33A HCA3A 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell
CC30A CC32A CC33A HCA3A 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell
CC31A CC32A CC33A HCA3A 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell
CC32A CC32A CC33A HCA3A 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell
CC33A CC32A CC33A HCA3A 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 HCA3A 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell, tf2m viv
CC325B CC325B CC33A HCA3A 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell, tf2m viv
OC305A CC325B CC33A HCA3A 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
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 HCA2A 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thp, viv
HCA2A CC326A CC326A HCA2A 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thp, viv
HCA2A CC326A CC326A CC326A 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thp, viv
OC30A CC326A CC326A HCA2A 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thp viv
HCA2A CC326A CC33A HCA3A 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell, me-thp viv
CC326A CC326A CC33A HCA3A 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell, me-thp viv
OC30A CC326A CC33A HCA3A 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
HCA3A CC33A CC33A HCA3A 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 HCA2A 0.28400 3 0.0 ! DMET, viv
HCA2A CC32A CC32A OC30A 0.19000 3 0.0 ! alkane, 4/98, yin and mackerell
OC30A CC32A CC33A HCA3A 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell
HCA2A CC32A OC30A CC32A 0.28400 3 0.0 ! DEET, diethylether, alex
HCA3A CC33A OC30A CC32A 0.28400 3 0.0 ! DEET, diethylether, alex
HCA2A CC32A OC30A CC33A 0.28400 3 0.0 ! DEET, diethylether, alex
HCA3A 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
HCA1A 0.0 -0.0450 1.3400 ! alkane,isobutane 1/5/05 viv
HCA2A 0.0 -0.0350 1.3400 ! alkane,propane 11/16/04 viv
HCA3A 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
END
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* \\\\\\\ CHARMM36 All-Hydrogen Lipid Parameter File ///////
* All comments and questions should be submitted to the
* parameter forum at the CHARMM website: www.charmm.org
*
!references
!
!Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph
!W. O'Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor
!Vorobyov, Alexander D. MacKerell, Jr. and Richard W. Pastor "Update of
!the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six
!Lipid Types" J. Phys. Chem. B 2010, 114, 7830-7843
!
! PUFA Modifications
!Jeffery B. Klauda, Viviana Monje, Taehoon Kim, and Wonpil Im. "Improving
!the CHARMM Force Field for Polyunsaturated Fatty Acid Chains" J. Phys. Chem. B.
!2012 ASAP http://dx.doi.org/10.1021/jp304056p
ATOMS
MASS -1 HL 1.00800 ! polar H (equivalent to protein H)
MASS -1 HCL 1.00800 ! charged H for PE (equivalent to protein HC)
MASS -1 HOL 1.00800 ! Nucleic acid phosphate hydroxyl proton
MASS -1 HAL1 1.00800 ! alphatic proton
MASS -1 HAL2 1.00800 ! alphatic proton
MASS -1 HAL3 1.00800 ! alphatic proton
MASS -1 HEL1 1.00800 ! for alkene; RHC=CR
MASS -1 HEL2 1.00800 ! for alkene; H2C=CR
MASS -1 HBL 1.00800 ! POPS SER backbone H
MASS -1 CL 12.01100 ! carbonyl C (acetic acid/methyl acetate)
MASS -1 CTL1 12.01100 ! sp3 carbon with 1 H (-CH1-)
MASS -1 CTL2 12.01100 ! carbon of methylene group (-CH2-)
MASS -1 CTL3 12.01100 ! carbon of methyl group (-CH3)
MASS -1 CTL5 12.01100 ! carbon of methyl group (-CH3) for tetramethylammonium
MASS -1 CEL1 12.01100 ! for alkene; RHC=CR
MASS -1 CEL2 12.01100 ! for alkene; H2C=CR
MASS -1 CCL 12.01100 ! for POPS
MASS -1 NTL 14.00700 ! ammonium nitrogen
MASS -1 NH3L 14.00700 ! nitrogen phosphatidylethanolamine
MASS -1 OBL 15.99940 ! acetic acid carboxyl oxygen (e. to protein OB)
MASS -1 OCL 15.99940 ! acetate oxygen
MASS -1 OSL 15.99940 ! ester oxygen
MASS -1 O2L 15.99940 ! Nucleic acid =O in phosphate or sulfate
MASS -1 OHL 15.99940 ! Nucleic acid phosphate hydroxyl oxygen
MASS -1 OSLP 15.99940 ! Phosphate oxygen, to avoid conflict with methylacetate type O
MASS -1 PL 30.97400 ! phosphorus
MASS -1 SL 32.06000 ! Sulfate sulfur
MASS -1 CRL1 12.01100 ! sp3 carbon with 1 H on a ring (-CH1-) for sterols
MASS -1 CRL2 12.01100 ! carbon of methylene group on a ring (-CH2-) for sterols
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
CTL1 CCL 200.0 1.522 ! for POPS
OBL CL 750.0 1.220 ! methyl acetate
OCL CL 525.0 1.260 ! acetate, protein
OCL CCL 525.0 1.260 ! for POPS
OSL CL 150.0 1.334 ! methyl acetate
OSLP 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
CTL1 HBL 330.00 1.080 ! for POPS
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
CTL3 OSLP 340.0 1.43 !
CTL2 OSLP 340.0 1.43 !
CTL1 OSLP 340.0 1.43 !
OSL PL 270.0 1.60 ! phosphate
OSLP PL 270.0 1.60 !
O2L PL 580.0 1.48 ! phosphate
OHL PL 237.0 1.59 ! phosphate
NH3L HCL 410.0 1.04 ! ethanolamine
NH3L CTL1 200.0 1.48 ! for POPS
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
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
CTL2 CTL1 CCL 52.0 108.00 ! for POPS
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
OSL CL CTL1 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
OCL CCL OCL 100.0 124.0 70.0 2.2250 ! for POPS
OCL CCL CTL1 40.0 118.0 50.0 2.3880 ! for POPS
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 CTL1 75.700 110.10 ! acetic acid, PIP
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
OSLP CTL1 CTL1 75.700 110.10 ! acetic acid, PIP
OSLP CTL1 CTL2 75.700 110.10 ! acetic acid
OSLP CTL1 CTL3 75.700 110.10 ! acetic acid
OSLP CTL2 CTL1 75.700 110.10 ! acetic acid
OSLP CTL2 CTL2 75.700 110.10 ! acetic acid
OSLP 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
HAL1 CTL1 OSLP 60.0 109.5 ! phosphate
HAL2 CTL2 OSLP 60.0 109.5 ! phosphate
HAL3 CTL3 OSLP 60.0 109.5 ! phosphate
CTL1 OSL PL 20.0 120.0 35.0 2.33 ! phosphate, PIP
CTL2 OSL PL 20.0 120.0 35.0 2.33 ! phosphate
CTL3 OSL PL 20.0 120.0 35.0 2.33 ! phosphate
CTL1 OSLP PL 20.0 120.0 35.0 2.33 ! phosphate, PIP
CTL2 OSLP PL 20.0 120.0 35.0 2.33 ! phosphate
CTL3 OSLP 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
OSLP PL OSLP 80.0 104.3 ! phosphate
OSLP PL O2L 98.9 111.6 ! phosphate
OSLP 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
CTL2 NTL CTL2 60.0 109.5 26. 2.466 ! tetraethylammonium, from CTL5 NTL CTL2
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
HBL CTL1 CCL 50.000 109.50 ! for POPS
HBL CTL1 CTL2 35.000 111.00 ! for POPS
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 CTL1 30.0 109.50 20.00 2.074 ! for POPS
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
NH3L CTL1 CCL 43.7 110.00 ! for POPS
NH3L CTL1 CTL2 67.7 110.00 ! for POPS
NH3L CTL1 HBL 51.5 107.50 ! for POPS
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
CTL3 CTL1 CTL3 58.350 113.50 11.16 2.561 ! glycerol
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 CTL1 75.700 110.10 ! glycerol, PIP
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
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
CEL1 CTL2 CEL1 30.0 114.0 ! 1,4-dipentene, adm jr., 2/00
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
OCL CCL CTL1 NH3L 3.20 2 180.00 ! for POPS
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
OSLP CL CTL2 HAL2 0.00 6 180.00 ! acetic acid
OSLP 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
X CTL1 CCL X 0.05 6 180.00 ! for POPS
HAL2 CTL2 CL OHL 0.00 6 180.00
HAL3 CTL3 CL OHL 0.00 6 180.00
PL OSLP CTL2 CTL1 0.407 2 0.00 ! Phos-gly, 8/05
PL OSLP CTL2 CTL1 0.241 1 180.00 ! Phos-gly, 8/05
PL OSLP CTL2 CTL2 0.407 2 0.00 ! Phos-gly, 8/05
PL OSLP CTL2 CTL2 0.241 1 180.00 ! Phos-gly, 8/05
OSL PL OSL CTL1 1.20 1 180.00 ! phosphate, new NA, 4/98, adm jr., PIP
OSL PL OSL CTL1 0.10 2 180.00 ! phosphate, new NA, 4/98, adm jr., PIP
OSL PL OSL CTL1 0.10 3 180.00 ! phosphate, new NA, 4/98, adm jr., PIP
OSLP PL OSLP CTL1 1.20 1 180.00 ! phosphate, new NA, 4/98, adm jr., PIP
OSLP PL OSLP CTL1 0.10 2 180.00 ! phosphate, new NA, 4/98, adm jr., PIP
OSLP PL OSLP CTL1 0.10 3 180.00 ! phosphate, new NA, 4/98, adm jr., PIP
OSLP PL OSLP CTL2 1.20 1 180.00 ! phosphate, new NA, 4/98, adm jr.
OSLP PL OSLP CTL2 0.10 2 180.00 ! phosphate, new NA, 4/98, adm jr.
OSLP PL OSLP CTL2 0.10 3 180.00 ! phosphate, new NA, 4/98, adm jr.
O2L PL OSLP CTL2 0.10 3 0.00 ! phosphate, new NA, 4/98, adm jr.
O2L PL OSL CTL2 0.10 3 0.00 ! phosphate, new NA, 4/98, adm jr.
OSLP PL OSLP CTL3 1.20 1 180.00 ! phosphate, new NA, 4/98, adm jr.
OSLP PL OSLP CTL3 0.10 2 180.00 ! phosphate, new NA, 4/98, adm jr.
OSLP PL OSLP CTL3 0.10 3 180.00 ! phosphate, new NA, 4/98, adm jr.
O2L PL OSLP CTL1 0.10 3 0.00 ! phosphate, new NA, 4/98, adm jr., PIP
O2L PL OSL CTL1 0.10 3 0.00 ! phosphate, new NA, 4/98, adm jr., PIP
O2L PL OSLP CTL3 0.10 3 0.00 ! 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 CTL1 0.95 2 0.00 ! terminal phosphate, PIP
OHL PL OSL CTL1 0.50 3 0.00 ! terminal phosphate, PIP
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
OHL PL OSLP CTL2 0.95 2 0.00 ! terminal phosphate
OHL PL OSLP CTL2 0.50 3 0.00 ! terminal phosphate
OHL PL OSLP CTL3 0.95 2 0.00 ! terminal phosphate
OHL PL OSLP 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.
X CTL1 OSLP X 0.00 3 0.00 ! phosphate, new NA, 4/98, adm jr.
X CTL2 OSLP X 0.00 3 0.00 ! phosphate, new NA, 4/98, adm jr.
X CTL3 OSLP X 0.00 3 0.00 ! phosphate, new NA, 4/98, adm jr.
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 0.000 6 0.00 ! glycerol & propl ester, 6/07
CTL2 CTL2 CL OSL 0.030 3 180.00 ! glycerol & propl ester, 6/07
CTL2 CTL2 CL OSL 0.432 2 180.00 ! glycerol & propl ester, 6/07
CTL2 CTL2 CL OSL 0.332 1 0.00 ! glycerol & propl ester, 6/07
CTL3 CTL2 CL OSL 0.000 6 0.00 ! glycerol & propl ester, 6/07
CTL3 CTL2 CL OSL 0.030 3 180.00 ! glycerol & propl ester, 6/07
CTL3 CTL2 CL OSL 0.432 2 180.00 ! glycerol & propl ester, 6/07
CTL3 CTL2 CL OSL 0.332 1 0.00 ! glycerol & propl ester, 6/07
CTL3 CTL2 CTL2 CL 0.000 5 180.00 ! propyl ester, 6/07
CTL3 CTL2 CTL2 CL 0.317 3 180.00 ! propyl ester, 6/07
CTL3 CTL2 CTL2 CL 0.557 2 0.00 ! propyl ester, 6/07
CTL3 CTL2 CTL2 CL 0.753 1 0.00 ! propyl ester, 6/07
CTL2 CTL2 CTL2 CL 0.000 5 180.00 ! propyl ester, 6/07
CTL2 CTL2 CTL2 CL 0.317 3 180.00 ! propyl ester, 6/07
CTL2 CTL2 CTL2 CL 0.557 2 0.00 ! propyl ester, 6/07
CTL2 CTL2 CTL2 CL 0.753 1 0.00 ! propyl ester, 6/07
OSL CTL2 CTL1 OSL -0.429 4 60.00 ! glycerol, 8/08
OSL CTL2 CTL1 OSL 0.614 3 0.00 ! glycerol, 8/08
OSL CTL2 CTL1 OSL -0.115 2 60.00 ! glycerol, 8/08
OSL CTL2 CTL1 OSL 0.703 1 180.00 ! glycerol, 8/08
OSLP CTL2 CTL1 OSL 0.000 4 0.00 ! Fit to QM, theta2, 07/08 jbk
OSLP CTL2 CTL1 OSL 0.607 3 180.00 ! Fit to QM, theta2, 07/08 jbk
OSLP CTL2 CTL1 OSL 0.254 2 60.00 ! Fit to QM, theta2, 07/08 jbk
OSLP CTL2 CTL1 OSL 2.016 1 180.00 ! Fit to QM, theta2, 07/08 jbk
OSLP CTL2 CTL2 OSL 0.000 4 0.00 ! Fit to QM, theta2, 07/08 jbk
OSLP CTL2 CTL2 OSL 0.607 3 180.00 ! Fit to QM, theta2, 07/08 jbk
OSLP CTL2 CTL2 OSL 0.254 2 60.00 ! Fit to QM, theta2, 07/08 jbk
OSLP CTL2 CTL2 OSL 2.016 1 180.00 ! Fit to QM, theta2, 07/08 jbk
CTL3 CTL1 CTL2 OSL 0.000 3 0.00 ! glycerol, theta3
CTL2 CTL1 CTL2 OSL 0.000 3 0.00 ! glycerol, theta3
CTL3 CTL2 CTL2 OSL 0.000 3 0.00 ! glycerol, theta3
CTL2 CTL2 CTL2 OSL 0.000 3 0.00 ! glycerol, theta3
CL OSL CTL1 CTL2 0.000 4 0.00 ! glycerol, beta1 6/07
CL OSL CTL1 CTL2 0.150 3 180.00 ! glycerol, beta1 6/07
CL OSL CTL1 CTL2 1.453 2 180.00 ! glycerol, beta1 6/07
CL OSL CTL1 CTL2 0.837 1 180.00 ! glycerol, beta1 6/07
CL OSL CTL1 CTL3 0.000 4 0.00 ! glycerol, beta1 6/07
CL OSL CTL1 CTL3 0.150 3 180.00 ! glycerol, beta1 6/07
CL OSL CTL1 CTL3 1.453 2 180.00 ! glycerol, beta1 6/07
CL OSL CTL1 CTL3 0.837 1 180.00 ! glycerol, beta1 6/07
CL OSL CTL2 CTL1 0.267 3 180.00 ! glycerol, gamma1 6/07
CL OSL CTL2 CTL1 0.173 2 0.00 ! glycerol, gamma1 6/07
CL OSL CTL2 CTL1 0.781 1 180.00 ! glycerol, gamma1 6/07
X CTL2 NTL X 0.26 3 0.00 ! tetramethylammonium
X CTL5 NTL X 0.23 3 0.00 ! tetramethylammonium
X CTL1 NH3L X 0.10 3 0.00 ! for POPS
X CTL2 NH3L X 0.10 3 0.00 ! ethanolamine
NH3L CTL2 CTL2 OHL 0.7 1 180.00 ! ethanolamine
NH3L CTL2 CTL2 OSLP 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 OSLP 3.3 1 180.00 ! choline, 12/92
NTL CTL2 CTL2 OSLP -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
!alkane CCCC dihedrals based on pentane, heptane and hexane vdz/vqz/ccsd(t) QM data
CTL3 CTL2 CTL2 CTL3 0.060 2 0.00 ! alkane, 7/08, jbk
CTL3 CTL2 CTL2 CTL3 0.035 5 0.00 ! alkane, 7/08, jbk
CTL2 CTL2 CTL2 CTL3 0.162 2 0.00 ! alkane, 7/08, jbk
CTL2 CTL2 CTL2 CTL3 0.047 3 180.00 ! alkane, 7/08, jbk
CTL2 CTL2 CTL2 CTL3 0.105 4 0.00 ! alkane, 7/08, jbk
CTL2 CTL2 CTL2 CTL3 0.177 5 0.00 ! alkane, 7/08, jbk
CTL2 CTL2 CTL2 CTL2 0.101 2 0.00 ! alkane, 7/08, jbk
CTL2 CTL2 CTL2 CTL2 0.142 3 180.00 ! alkane, 7/08, jbk
CTL2 CTL2 CTL2 CTL2 0.074 4 0.00 ! alkane, 7/08, jbk
CTL2 CTL2 CTL2 CTL2 0.097 5 0.00 ! alkane, 7/08, 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 0.4500 1 180.00 ! 2-butene, adm jr., 4/04
X CEL1 CEL1 X 8.5000 2 180.00 !
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
!alkene update, 2004,2009
CEL1 CEL1 CTL2 HAL2 0.3000 3 180.00 !2-butene, adm jr., 4/04
CEL1 CEL1 CTL3 HAL3 0.3000 3 180.00 !2-butene, adm jr., 4/04
!CEL1 CEL1 CTL2 CTL3 0.9000 1 180.00 !2-pentene and 3-heptene
!CEL1 CEL1 CTL2 CTL3 0.2000 2 180.00 !2-pentene and 3-heptene
CEL1 CEL1 CTL2 CTL3 0.9100 1 180.0 !2-hexene, adm jr., 11/09, end fix jbk
CEL1 CEL1 CTL2 CTL3 0.1800 2 180.0 !2-hexene, adm jr., 11/09
CEL1 CEL1 CTL2 CTL3 0.1700 3 180.0 !2-hexene, adm jr., 11/09
CEL1 CEL1 CTL2 CTL2 0.9100 1 180.0 !2-hexene, adm jr., 11/09
CEL1 CEL1 CTL2 CTL2 0.1800 2 180.0 !2-hexene, adm jr., 11/09
CEL1 CEL1 CTL2 CTL2 0.1700 3 180.0 !2-hexene, adm jr., 11/09
CEL1 CTL2 CTL2 CL 0.1400 1 180.0 !2-hexene, adm jr., 11/09, add jbk for DHA
CEL1 CTL2 CTL2 CL 0.1700 2 0.0 !2-hexene, adm jr., 11/09, add jbk for DHA
CEL1 CTL2 CTL2 CL 0.0500 3 180.0 !2-hexene, adm jr., 11/09, add jbk for DHA
CEL1 CTL2 CTL2 CTL2 0.1400 1 180.0 !2-hexene, adm jr., 11/09
CEL1 CTL2 CTL2 CTL2 0.1700 2 0.0 !2-hexene, adm jr., 11/09
CEL1 CTL2 CTL2 CTL2 0.0500 3 180.0 !2-hexene, adm jr., 11/09
CEL1 CTL2 CTL2 CTL3 0.1400 1 180.0 !2-hexene, adm jr., 11/09
CEL1 CTL2 CTL2 CTL3 0.1700 2 0.0 !2-hexene, adm jr., 11/09
CEL1 CTL2 CTL2 CTL3 0.0500 3 180.0 !2-hexene, adm jr., 11/09
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, jbk., 9/2010
! for CIS double bonds in polyunsaturated lipids (default)
CEL1 CEL1 CTL2 CEL1 0.850 1 180.00 !2,5-diheptane
CEL1 CEL1 CTL2 CEL1 0.300 2 180.00 !2,5-diheptane
CEL1 CEL1 CTL2 CEL1 0.260 3 0.00 !2,5-diheptane
CEL1 CEL1 CTL2 CEL1 0.096 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
OCL X X CCL 96.00 0 0.00 ! for POPS
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
HBL 0.0 -0.022 1.3200 ! for POPS