[gmx-users] introducing "HISE" to gromos43a1

[Sajad Ahrari]

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

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Justin A. Lemkul, Ph.D.
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