On 4/18/16 9:05 AM, Nikhil Maroli wrote:
Hi thanks for your suggestion, When i give both same name in mdp and top it gives an error Atom index (123) in position_restraints out of bounds (1-122). This probably means that you have inserted topology section "position_restraints this is my topology file structure ; Include forcefield parameters #include "toppar/charmm36.itp" #include "toppar/PROA.itp" #include "toppar/PROB.itp" #include "toppar/PROC.itp" #include "toppar/PROD.itp" #include "toppar/PROE.itp" #include "toppar/PROF.itp" #include "toppar/PROG.itp" #include "toppar/PROH.itp" ; Ligand position restraints #ifdef POSRES_PROT #include "posre_cpn.itp" #endif
You can't do this. Restraints are applied on a per-moleculetype basis. http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds
#include "toppar/POPE.itp" #include "toppar/TIP3.itp" #include "toppar/SOD.itp" #include "toppar/CLA.itp" PROA....PROH are identical cyclic peptide rings ,posre_cpn is restrain file for c-alpha atoms in all the rings . in mpd file define = -DPOSRES_PROT when i give only define = -DPOSRES in mdp grompp running successfully but in gmx energy no restrain energy --
Because it's doing precisely nothing, so no error can be raised and no restraints are applied because of the mismatch between define and #ifdef.
-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.
