[gmx-users] introducing "HISE" to gromos43a1

Sajad Ahrari sajadahrari at yahoo.com
Sat Jan 25 21:18:24 CET 2014

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.

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

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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