On 1/16/14, 9:51 AM, Mahboobeh Eslami wrote:
hi GMX user please help me i want to simulated a protein-ligand complex. This complex has previously been studied experimentally. I draw and opt this ligand by Gaussian software. i get the native protein of RCSB. i dock my ligand in the active site of the protein and select the best pose. This pose was almost close to the experimental structure, but not much. i run 10ns simulation but the simulation results were not close to the experimental results, especially conformation of the ligand in the active site of the protein.
You have two potential problems, either the ligand topology or its initial pose. Run a simulation of the experimental complex, and if the ligand's position deviates similarly, then your topology is of poor quality. If it is reasonable, then your docked pose is of insufficient quality ("almost close...but not much" does not inspire confidence).
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ================================================== -- 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.
