[gmx-users] Re: Problem with Amber99SB-ILDN ff

Justin Lemkul jalemkul at vt.edu
Mon Jul 8 13:03:59 CEST 2013

On 7/8/13 7:00 AM, Melchor S. wrote:
> Ok, I will try it. Thank you. But when a chain starts with MET why this
> nomenclature is not needed? Because with MET works fine like any other
> forcefield.

There are a lot of variables at play here that you haven't described (Gromacs 
version, pdb2gmx command, snippet of the input .pdb file where the chains 
switch), so I'm only guessing here.  I believe in the 4.6.x series, pdb2gmx 
should not technically need the N and C prefixes.  If you're using one of these 
versions, then there is something wrong with (1) the way you're telling pdb2gmx 
to identify chains or (2) the input .pdb file itself.



Justin A. Lemkul, Ph.D.
Postdoctoral Associate

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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