On 6/1/15 10:57 AM, Kevin C Chan wrote:
Dear Users, I am testing with OPLSSaa force-field of proline. First I arbitrarily extract a single PRO from a pdb and fed into pdb2gmx. The resulted gro and top are however not suitable for further grompp (even minimization). The error messages are as follows: ERROR 1 [file topol.top, line 161]: No default Ryckaert-Bell. types When I look into the line 161, it refers to a dihedral term concerning (CD N CA C) which is not able to be found in ffbonded.itp. However, other dihedral terms such as (CD N CA CB) or (CD N CA HA) which are also not found in itp do not report such error and I was successful to grompp after commenting out the line 161. Why would this happen?
Did you choose the proper "PRO-ZWITTERION-*" termini when running pdb2gmx? -Justin -- ================================================== 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.
