On 1/9/17 2:09 AM, Shanmuga Priya V.G wrote:
Dear Gromacs Users, I have a insilico model of Mycobacterium tuberculosis cell wall (surface) protein which has no transmembrane helices. Which Gromacs tutorials should I follow for MD studies to know about its conformational stability and latter for protein - ligand studies. Kindly guide me
This depends on whether or not the protein has any significant interaction with the cell wall. If it does, you'll have to model it as a peripheral membrane protein (e.g. bound to, but not embedded in, the membrane). Otherwise, if it is distant from the cell wall, it's like any normal protein-in-water system or protein-ligand complex, for which any number of tutorials exist (just ask Google!).
-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.
