[gmx-users] g_membed itp file

[Justin Lemkul]

On 6/4/14, 4:06 AM, h.alizadeh at znu.ac.ir wrote:
> Dear GROMACS users,
> I'm a new GROMACS user and I would like to apologize for my basic question.
> I want to use g_membed to insert protein in membrane according to Wolf's
> paper manual. I have the pdb, mdp and top files in my directory, but when I
> enter the command
>
> grompp -f sample.mdp -c merged.gro -p merged.top -o input.tpr
>
> I face with this fatal error:
> Fatal error:
> Topology include file "ffoplsaalipid.itp" not found
>
> Now I want to know how can I create this itp file?

How did you generate the .top file that includes this .itp file?  It looks like 
it relies on some modified version of the OPLS-AA force field, with added lipid 
parameters.  That's not going to be standard in Gromacs, so it's likely 
dependent upon some external source.  Given the naming convention of the file, 
it was probably designed for some old version of Gromacs, but can certainly be 
made to work if you actually obtain the necessary force field files.

-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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