On 2/9/16 10:54 AM, Sana Saeed wrote:
hi gmx usersi want to find out absolute binding free energy of protein ligand complex. fisrt i performed docking and selected best poses and then i made topology file of ligand with PRODRGserver. and then included itp file of ligand in Protein topology file (from pdb2gmx) , also made complex.gro as in tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html . can i use these complex files for MD for absolute binding free energy? in some tutorials the topology file of complex is quite differently organised. please guide me, i am following decoupling and coupling steps from http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme
PRODRG topologies are inaccurate for even simple MD simulations. Using it for a free energy calculation is certain to result in junk.
-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.
