On 6/6/17 2:12 AM, RAHUL SURESH wrote:
Dear Users *Exp procedure:* I have simulated the protein monomer for 150ns. Using the 150ns conformer, ligand is docked to the protein using autodock and the simulation is carried out for 50ns. *Analysis:* Is it possible to compare my RMSD, RMSF, ROG analysis of complex system with that of monomer? If yes which part of the monomer trajectory should be considered.?
This is up to you to determine in light of whatever your goals are in running the simulation. What are you trying to test or determine? Unless the protein's stability is seriously impacted by the ligand, RMSD and Rg are useless. RMSF might be useful if there are motions that are amplified or damped by ligand binding. Run the analysis and see what happens on a per-residue basis.
-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.
