[gmx-users] OPLS parametes for cholesterol
Yang Ye
leafyoung at yahoo.com
Tue Sep 18 17:35:31 CEST 2007
Hi, Valentin
Could you describe how you obtained it? So it carries more credibility
as well as makes it citable for you.
Regards,
Yang Ye
On 9/18/2007 9:00 PM, Valentin Gogonea wrote:
> 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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