[gmx-users] OPLS parametes for cholesterol
Valentin Gogonea
v.gogonea at csuohio.edu
Tue Sep 18 18:31:23 CEST 2007
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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