On 12/25/14 5:03 PM, Hassan Aaryapour wrote:
Dear Gromacs Users How can I find and score protein-ligand binding poses and choose the best pose or frame from the trajectory file after doing a Molecular dynamics simulation of 40ns?
"Best" is a qualitative assessment that should be driven by objective, quantitative metrics. Decide how you want/need to analyze the interactions of the ligand with the protein, and the pose that is "best" is probably the one that captures most/all of the principle features (contacts, hydrogen bonds, dihedral angles, etc).
-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.
