[gmx-users] how to name HIS in the input pdb for the pdb2gmx

Justin Lemkul jalemkul at vt.edu
Sun Apr 26 05:08:53 CEST 2015

On 4/25/15 11:05 PM, Brett wrote:
> Dear All,
> For gromacs, for HIS residues there are HISD,HISE and HISH. In the original PDB file, are HIS residues are written as HIS. If based on necessity, I change exactly some HIS to HISD, some HIS to HISE and some HIS to HISH,the coordinate lines contaning HISD,HISE and HISH will not aling with all the other coordinate lines. Does pdb2gmx recognize these non-aligned coordinate lines? Or what other strategy you recommend me to take so that pdb2gmx can recognize HISD,HISE and HISH?

Do the replacement properly and don't screw up column alignment.  It needs to be 
correct for proper interpretation of the coordinates.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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