[gmx-users] introducing "HISE" to gromos43a1

[Sajad Ahrari]

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?

-Justin

>
> 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
>
> --
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> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
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-- 
==================================================

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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