On 6/21/17 11:39 AM, Jose Borreguero wrote:
Hi Justin, Thanks for your quick reply! This means x2top is not finding or using the right force constant value, right? I did add the bond info into file ffbonded.itp of the oplsa.ff/ directory (https://goo.gl/z5UMot) . I also included the types in file atomtypes.atp and the non bonded info in ffnonbonded.itp file. Maybe related to this issue is this line also found in the output .top file: #include " ./oplsaa.ff/forcefield.itp" This line should not be necessary because the .top file contains all information. Does the line mean that the bond information in the output .top file is overridden with that gmx later finds under ./oplsaa.ff ? If so, then the particular value of the force constant in the .top file would be irrelevant and my problem would be solved! :)
Any value found in the .top overrides the force field. Any blank in the topology is referenced from ffbonded.itp. Anything missing after that generates a fatal error in grompp. Use -noparam when running x2top if everything is accounted for in the force field parameter files.
-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.
