[gmx-users] OPLS parametes for cholesterol
Yang Ye
leafyoung at yahoo.com
Tue Sep 18 18:54:13 CEST 2007
Hi, Valentin
This write-up is good so people will use it with caution.
Regards,.
Yang Ye
On 9/19/2007 12:31 AM, Valentin Gogonea wrote:
> Hi Yang,
>
> To describe the bonding interactions I used atom types from the OPLS
> force field (.atp file). I picked the atom type based on chemical
> environment (eg sp3/sp2 for C or being involved in a specific
> functional group). So I did not create new atom types. The partial
> charges are the default ones given in ffoplsaanb.itp (probably
> adjusted adhoc a bit to sum up to zero). I did not check if the
> geometry fits a QM geometry, but after a MM geometry optimization in
> gas phase it looked OK. If you need an accurate ff for cholesterol you
> definitely will have to refine the parameters and charges but the set
> I gave you should be a good start. My interest was just to have
> cholesterol into a POPC bilayer and I did not need to look at specific
> interactions of CHL with POPC or water. So this ff was ok for me but
> may not be satisfactory for your purpose.
>
> I hope this helps.
>
> Valentin
> On Sep 18, 2007, at 11:35 AM, Yang Ye wrote:
>
>> 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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>>>
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>>
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