On 7/28/17 2:54 PM, Mohammad Zahidul Hossain Khan wrote:
Dear User I have protein-ligand system. I have basic idea for energy minimization.mdp parameter. ; integrator = steep emtol = 10.0 emstep = 0.01 nsteps = 500 energygrps = Protein OAI ; nstlist = 1 cutoff-scheme = Verlet ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 rvdw = 1.0 pbc = xyz but I have not idea how to write the parameter *where all the backbone heavy atoms of the protein have to be constrained with an elastic constant of 50 kcal /mol Å -2 and the other atoms should be free.* Does anyone know how to write elastic constant parameter in energy minimization mdp file.
Restraints are a topological construct, not one that is (directly) specified in the .mdp file. Run your protein coordinates (only) through gmx genrestr and choose the backbone as the output group. Specify the desired force constant on the command line (make sure to convert your value to kJ mol^-1 nm^-2). Save the new position restraint file to something like "posre_bb.itp" and #include it in the topology in the protein's [moleculetype] section, e.g.
#ifdef POSRES_BB #include "posre_bb.itp" #endif Then specify "define = -DPOSRES_BB" in the .mdp file. -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.
