On 10/28/15 9:57 AM, Joan Clark Nicolas wrote:
Dear gmx users, I am trying to run MD calculations on a protein-ligand system using Virtual Sites, but as I generate my protein and ligand topologies separately (with pdb2gmx and acpype, respectively), the VS for the ligand are not generated. Does anyone know a way to generate the VS for the ligand without adding it to the force field?
One can define any [ virtual_sites* ] directive manually in the topology. pdb2gmx can build some types of virtual sites, but you'd have to tell us specifically what it is you're trying to do if you want anything really useful. Soon I will upload a patch that will make virtual site construction easier, and intrinsic to pdb2gmx. I just need to find the time to work out the kinks...
-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.
