On 7/15/15 11:53 AM, anu chandra wrote:
Dear Gromcacs users, I have carried out 25 ns simulation of membrane-protein systems. Now, I would like to do position restrain of ions for the next 1-2 ns. I have KCl in my system. I used ' genrestr ' for generating the position restrain for ions using the following command - genrestr -f md50.gro -o ions-rest.itp I have included ions-rest.itp in the .top file with proper ' ifdef ' term as mention in tutorials. Unfortunately, the grommp shows error message - " Atom index (2) in position_restraints out of bounds (1-1). This probably means that you have inserted topology section "position_restraints" in a part belonging to a different molecule than you intended to" . I have seen from Gromcas mail list that many faced similar issues and this usually comes from the mismatch in atom indices. Unfortunately, I could not find complete solution for it yet. Few queries in this regard are, 1. How can I generate a position restrain file for ions or any set of molecules in the system? my topology file have following hierarchy, **************************************************************** ; This is a standalone topology file ; ; Created by: ; GROMACS: gmx pdb2gmx, VERSION 5.0.4 ; Executable: /usr/local/gromacs/bin/gmx ; Library dir: /usr/local/gromacs/share/gromacs/top ; Command line: ; gmx pdb2gmx -f step5_IP3R.pdb -ter ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include "charmm36-jun2015.ff/forcefield.itp" ; Include chain topologies #include "topol_Protein.itp" #include "topol_Protein2.itp" #include "topol_Protein3.itp" #include "topol_Protein4.itp" #include "POPC.itp" ; Include water topology #include "charmm36-jun2015.ff/tip3p.itp" ; Include topology for ions #include "charmm36-jun2015.ff/ions.itp" [ system ] ; Name Titile [ molecules ] ; Compound #mols Protein 1 Protein2 1 Protein3 1 Protein4 1 POPC 295 POT 85 CL 122 SOL 24892 **************************************************************************** 2. Where all I can use the .itp file for a particular group generate with ' genrestr' command?
Restraints are applied on a per-moleculetype basis; hence genrestr is very limited in what it can do (multiple molecules won't work without considerable effort).
The only way to restrain the ions within this setup is to modify ions.itp to specify restraints within the relevant [moleculetype] directives.
-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.
