[gmx-users] introducing "HISE" to gromos43a1
samanshahriyari at yahoo.com
Sat Jan 25 17:07:19 CET 2014
thank you for answering. your instruction with "aminoacids.r2b file", helped. this time i am having the following problem;
Program pdb2gmx, VERSION 4.6.3
Source code file: /usr/local/Software/gromacs-4.6.3/src/kernel/pdb2gmx.c, line: 727
Atom OXT in residue TYR 363 was not found in rtp entry TYR with 18 atoms
while sorting atoms.
any suggestion on dealing with OXT?
On Saturday, January 25, 2014 4:27 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
On 1/25/14, 7:18 AM, Saman Shahriyari wrote:
> Hello dears i am trying to do some analysis on a trajectory by gromos43a1ff.
> but as i run pdb2gmx, an error shows up that the "HISE" residue is not known
> to this forcefield. how can i deal with this issue? can i be introducing the
> parameters of "HISE" to gromos43a1? if so, how can i get them and what the
> approach whould be?
HISE is just epsilon-protonated histidine, which Gromos96 force fields call
HISB. There is no need to add any sort of parameters; they're already there.
The aminoacids.r2b file should take care of the naming translation when running
pdb2gmx. If for some reason it doesn't, just rename the residues in the
coordinate 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
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