On 7/9/16 1:44 AM, Hassan Aaryapour wrote:
Dear Justin A. Lemkul, Thank you for answer. In US simulation the initial configurations were generated by translating ligand along the z-axis up to desired distance. Is it necessary to rotate my protein complex in correct orientation until protein exit side align with the z-axis and ligand could leave its binding
No alignment is necessary.
site? How can I find exit site in protein? The binding pocket is deeply buried inside the protein and not solvent accessible.
If there are multiple paths and nothing is known about the interactions, you would have to sample all of them. Usually the path is apparent, though. A deep channel is good news, because that means the reaction coordinate should be very easy to determine.
-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.
