[gmx-users] Re: Problem with Amber99SB-ILDN ff
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
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.
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
More information about the gromacs.org_gmx-users