[gmx-users] Error while trying to create a membrane-protein system

[Justin Lemkul]

On 5/29/14, 8:50 AM, Spyridon Vicatos wrote:
> I checked you question. In order to create my membed.tpr file, I used
>
> grompp -c prot_dppc.gro -p *system.top* -f membed.mdp *-o membed.tpr*
>
>
>
>
> None of the files contain water. Not prot_dppc.gro, not the system.top. As for
> membed.mpdb, I am not sure where to look at, to see if there are any "waters"
> option used.
>

The g_membed program assumes water is present (note that this assumption is 
stated in the help information).  As such, it calls routines that process the 
topology to look for SETTLE directives.

The solution is to solvate the membrane before inserting the protein.

-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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