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 -- ================================================== 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 ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.