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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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