[gmx-users] How to combine Slipid FF with amber FF?
jalemkul at vt.edu
Sun Aug 31 15:06:45 CEST 2014
On 8/31/14, 8:42 AM, Yorquant Wang wrote:
> I have done that according to your advice and when I do the command
> grompp, I get such a error:
> Fatal error:
> Atomtype NTL not found
> this is my top file:
> #include "amber99sb-ildn.ff/forcefield.itp"
> #include "POPC.itp"
> #include "protein-amber.itp"
> #include "amber99sb-ildn.ff/ions.itp"
> #include "amber99sb-ildn.ff/tip3p.itp"
You get the error because none of these files knows anything about Slipids
parameters except POPC.itp, which tries to use them. So grompp fails. See my
previous reply; you need to modify the force field.
> [ system ]
> ; Name
> membrane protein
> [ molecules ]
> ; Compound #mols
> protein 2
> POPC 72
> SOL 3337
> NA 18
> CL 22
> 2014-08-31 20:20 GMT+08:00 rajat desikan <rajatdesikan at gmail.com>:
>> Slipids are already compatible with Amber. Just download the proper
>> lipid.itp file (DPPC.itp, DMPC.itp, ...) from the Slipids website, and
>> include the below line in your .top after processing your protein with
>> pdb2gmx (and selecting some Amber FF).
>> ; Include lipid topology
>> #include "./DMPC.itp"
>> Of course, you can change the name of the lipid.itp according to the
>> lipids in your system.
>> The order in which this appears in your .top matters. If you add the
>> lipids to your simulation box and then solvate it, the above line must
>> come prior to the water.itp
>> On 8/31/14, Yorquant Wang <wangykoo at gmail.com> wrote:
>>> Hi all,
>>> I want to do a membrane protein simulation and I want to use amber
>>> for protein (my target protein contains many beta sheet secondary
>>> structures). But forcefield.ff file in the web:
>>> http://people.su.se/~jjm/Stockholm_Lipids/Downloads.html, contains only
>>> lipids parameter. I don't know how to conbined those lipid parameter
>>> with amber99sb-ildn.ff.
>>> Is there anybody who can help me? Thank you very much.
>>> Yukun Wang
>>> PhD candidate
>>> Institute of Natural Sciences && College of Life Science, Shanghai Jiao
>>> Tong University
>>> Cell phone: 13621806236.
>>> China Shanghai
>>> Gromacs Users mailing list
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>> Rajat Desikan (Ph.D Scholar)
>> Prof. K. Ganapathy Ayappa's Lab (no 13),
>> Dept. of Chemical Engineering,
>> Indian Institute of Science, Bangalore
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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