[gmx-users] introducing "HISE" to gromos43a1

Justin Lemkul jalemkul at vt.edu
Sat Jan 25 14:00:10 CET 2014



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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University of Maryland, Baltimore
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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