[gmx-users] introducing "HISE" to gromos43a1
jalemkul at vt.edu
Sat Jan 25 21:15:11 CET 2014
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
> 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 <mailto:jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
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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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