[gmx-users] OPLS parametes for cholesterol
Valentin Gogonea
v.gogonea at csuohio.edu
Tue Sep 18 15:00:03 CEST 2007
I have one. You have to insert it in the .rtp file and use pdb2gmx. I
relabeled the atoms. This may be inconvenient if you use a pdb file
with coordinates for cholesterol.
Valentin
[ CHL ]
[ atoms ]
CA opls_136 -0.120 0
HA1 opls_140 0.060 0
HA2 opls_140 0.060 0
CB opls_136 -0.120 1
HB1 opls_140 0.060 1
HB2 opls_140 0.060 1
CC opls_137 0.205 2
HC opls_140 0.060 2
O opls_154 -0.683 2
H opls_155 0.418 2
CD opls_136 -0.120 3
HD1 opls_140 0.060 3
HD2 opls_140 0.060 3
CE opls_141 0.000 3
CF opls_142 -0.115 4
HF opls_144 0.115 4
CG opls_136 -0.120 5
HG1 opls_140 0.060 5
HG2 opls_140 0.060 5
CH opls_137 -0.060 6
HH opls_140 0.060 6
CI opls_137 -0.060 7
HI opls_140 0.060 7
CJ opls_139 0.000 7
C1 opls_135 -0.180 8
H11 opls_140 0.060 8
H12 opls_140 0.060 8
H13 opls_140 0.060 8
CK opls_136 -0.120 9
HK1 opls_140 0.060 9
HK2 opls_140 0.060 9
CL opls_136 -0.120 10
HL1 opls_140 0.060 10
HL2 opls_140 0.060 10
CM opls_139 0.000 10
C2 opls_135 -0.180 11
H21 opls_140 0.060 11
H22 opls_140 0.060 11
H23 opls_140 0.060 11
CN opls_137 -0.060 12
HN opls_140 0.060 12
CO opls_136 -0.120 13
HO1 opls_140 0.060 13
HO2 opls_140 0.060 13
CP opls_136 -0.120 14
HP1 opls_140 0.060 14
HP2 opls_140 0.060 14
CQ opls_137 -0.060 15
HQ opls_140 0.060 15
CR opls_137 -0.060 16
HR opls_140 0.060 16
C3 opls_135 -0.180 17
H31 opls_140 0.060 17
H32 opls_140 0.060 17
H33 opls_140 0.060 17
CS opls_136 -0.120 18
HS1 opls_140 0.060 18
HS2 opls_140 0.060 18
CT opls_136 -0.120 19
HT1 opls_140 0.060 19
HT2 opls_140 0.060 19
CU opls_136 -0.120 20
HU1 opls_140 0.060 20
HU2 opls_140 0.060 20
CV opls_137 -0.060 21
HV opls_140 0.060 21
CZ opls_135 -0.180 22
HZ1 opls_140 0.060 22
HZ2 opls_140 0.060 22
HZ3 opls_140 0.060 22
C4 opls_135 -0.180 23
H41 opls_140 0.060 23
H42 opls_140 0.060 23
H43 opls_140 0.060 23
[ bonds ]
CA HA1
CA HA2
CA CB
CA CJ
CB HB1
CB HB2
CB CC
CC HC
CC O
CC CD
O H
CD HD1
CD HD2
CD CE
CE CF
CE CJ
CF HF
CF CG
CG HG1
CG HG2
CG CH
CH HH
CH CI
CH CN
CI HI
CI CJ
CI CK
CJ C1
C1 H11
C1 H12
C1 H13
CK HK1
CK HK2
CK CL
CL HL1
CL HL2
CL CM
CM HM
CM CN
CM CQ
CM C2
C2 H21
C2 H22
C2 H23
CN HN
CN CO
CO HO1
CO HO2
CO CP
CP HP1
CP HP2
CP CQ
CQ HQ
CQ CR
CR HR
CR C3
C3 H31
C3 H32
C3 H33
CR CS
CS HS1
CS HS2
CS CT
CT HT1
CT HT2
CT CU
CU HU1
CU HU2
CU CV
CV HV
CV CZ
CV C4
CZ HZ1
CZ HZ2
CZ HZ3
C4 H41
C4 H42
C4 H43
[ dihedrals ]
HF CF CG CH CHL_dih_HC_CT_CT_CT
[ impropers ]
CD CF CE CJ improper_Z_CA_X_Y
CE CG CF HF improper_Z_CA_X_Y
On Sep 18, 2007, at 7:24 AM, Jochen Hub wrote:
> Hi,
>
> does anyone know if there are is an OPLS topology for cholesterol
> around.
>
> Thanks a lot in advance,
> Jochen & Plamen
>
> --
> ************************************************
> Jochen Hub
> Max Planck Institute for Biophysical Chemistry
> Computational biomolecular dynamics group
> Am Fassberg 11
> D-37077 Goettingen, Germany
> Email: jhub[at]gwdg.de
> ************************************************
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