On Mon, Dec 16, 2013 at 4:06 PM, Sidath Wijesinghe <swij...@g.clemson.edu>wrote:
> Dear Friends, > > i have done a MD simulation using OPLS/AA in lammps which contains 7930 > atoms. > i want to run this in Gromacs > > so i followed this step > > g_x2top -f test.pdb -o np1.top -name np1 -ff oplsaa -pbc ( test.pdb is the > pdb i obtained from my simulation) > after that it was trying to find the parameters from > oplsaa.ff/atomname2type.n2t > There are 23 name to type translations in file oplsaa.ff > Generating bonds from distances... > > and i got an error as following > > Fatal error: > Could only find a forcefield type for 7100 out of 7930 atoms > For more information and tips for troubleshooting, please check the GROMACS > > i have no idea what and where i need to work on to solve this problem. > please be kind enough to help me out with this > > g_x2top is not magic, and it is only as smart as the information you provide it. The output indicates that 830 atoms are not described by the available entries in the .n2t file. Refer to http://www.gromacs.org/Documentation/File_Formats/.n2t_File for information. The screen output should indicate which atoms are problematic. You will have to amend the existing file, which by default only covers the most trivial of molecules. -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.