[gmx-users] How to combine Slipid FF with amber FF?
jalemkul at vt.edu
Sun Aug 31 15:04:57 CEST 2014
On 8/31/14, 6:59 AM, Yorquant Wang wrote:
> Hi all,
> I want to do a membrane protein simulation and I want to use amber FF
> 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.
You just need to combine the contents of ffbonded.itp and ffnonbonded.itp to
those same files in the parent protein force field. Copy and paste into the
relevant directives or (possibly, never tried it this way) rename the
ffbonded.itp and ffnonbonded.itp files from Slipids and simply #include them in
your .top after the #include statement for the force field. Not sure if that
will work, especially if new atom types are added.
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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