[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 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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