On 12/9/15 10:52 AM, Alex Mathew wrote:
Hello everyone, i wanted to perform a Protein-Ligand Simulation,i created .itp,psf,.par etc files for ligand and am able to make topol.top and conf.gro or the protein using pdb2gmx .Forcefield is CHARMM27 Now i im confused how to include ligand into my system.as per tutorial we are provided with .gro file but in case of charmm forcefiled i didnt get any .gro file.
You don't need a .gro file; GROMACS happily accepts most coordinate formats. Probably .pdb is the most convenient for moving from CHARMM to GROMACS.
Or just upload everything to CHARMM-GUI and have it build the system and give you all the inputs you need. Note that CHARMM27 is not a protein force field. What you're using is CHARMM22/CMAP.
-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.
