[gmx-users] introducing "HISE" to gromos43a1
sajadahrari at yahoo.com
Sun Jan 26 08:15:22 CET 2014
the .pdb file is derived from an already existing .xtc (most probably yielded by gromos43a1 forcefield). and through analysing of this .xtc i should be converting it to some .pdb files. i doubt if there is any way to ignore this atom while making the .pdb files if i can't do a thing about renaming issues?
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Saturday, January 25, 2014 11:43 PM
Subject: Re: [gmx-users] introducing "HISE" to gromos43a1
On 1/25/14, 3:11 PM, Sajad Ahrari wrote:
> in fact Tyr363 is the C-terminus and the command is;
> pdb2gmx -f MARKII.pdb -o MARKII.gro -p MARKII.top
> I have TPO (phospho-threonie 208) as the non-standards amino-acid. so i used
> your introduced "gromos43a1p.ff" for pdb2gmx command.
pdb2gmx should replace the OXT it finds with O2, per the *.c.tdb file. What
happens if you rename OXT to O2 or remove it altogether?
> On Saturday, January 25, 2014 11:04 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 1/25/14, 11:04 AM, Saman Shahriyari wrote:
> > dear Justin
> > 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
> > Fatal error:
> > 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?
> pdb2gmx thinks Tyr363 is the C-terminus. Is that correct? What is your exact
> command line? Do you have any nonstandard residues?
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
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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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