[gmx-users] introducing "HISE" to gromos43a1

[Saman Shahriyari]

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?
best,
Saman






On Saturday, January 25, 2014 4:27 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
 



On 1/25/14, 7:18 AM, Saman Shahriyari wrote:
> Hello dears i am trying to do some analysis on a trajectory by gromos43a1ff.
> but as i run pdb2gmx, an error shows up that the "HISE" residue is not known
> to this forcefield. how can i deal with this issue? can i be introducing the
> parameters of "HISE" to gromos43a1? if so, how can i get them and what the
> approach whould be?

HISE is just epsilon-protonated histidine, which Gromos96 force fields call 
HISB.  There is no need to add any sort of parameters; they're already there. 
The aminoacids.r2b file should take care of the naming translation when running 
pdb2gmx.  If for some reason it doesn't, just rename the residues in the 
coordinate file itself.

-Justin

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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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