[gmx-users] How to combine Slipid FF with amber FF?

[Justin Lemkul]

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

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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