On 3/24/15 10:30 AM, mah maz wrote:
Hi Justin, Thanks for your reply. As you guessed correctly, for making a topology file I used "g_x2top -f file.gro -o file.top -ff forcefield -noparam". I have a CNT system and I thought I should use g_x2top instead of pdb2gmx command. If I'm right, what may cause this error and what would be the solution?
Either the input coordinates are not suitable for constructing the topology, or the .n2t file is constructed incorrectly. The fact that g_x2top found atoms with zero bonds indicates that some atoms are outside all possible distance criteria, hence zero bonds.
-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.
