[gmx-users] How to combine Slipid FF with amber FF?
jalemkul at vt.edu
Sun Aug 31 15:05:57 CEST 2014
On 8/31/14, 8:20 AM, rajat desikan wrote:
> 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
This is not true. The only case where #include statement order matters is if
new parameters are introduced. For any other simply .itp files that #include a
new [moleculetype], order is irrelevant. Order of appearance in [molecules]
must, however, match the order of appearance in the coordinate file.
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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