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

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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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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