[gmx-users] Bug #554: pdb2gmx proton naming compliancy

Justin Lemkul jalemkul at vt.edu
Wed Dec 4 14:14:20 CET 2013

On 12/3/13 4:51 PM, Kibalchenko, Mikhail wrote:
> Dear Users,
> does anyone know what was the resolution of this bug?
> http://redmine.gromacs.org/issues/554
> How does one handle pdb2gmx with PDB files and avoid errors like this?
> Atom HB3 in residue ASP 2 was not found in rtp entry ASP with 14 atoms
> while sorting atoms.

Use the -ignh flag and have pdb2gmx rebuild the H positions.  If you need the 
original H coordinates, rename as needed to match the force field or create 
entries in xlateat.dat to do it for you.



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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