Re: [gmx-users] evaluation of influence of pH on the stability of protein
On 8/29/16 3:10 PM, Mahboobeh Eslami wrote: Hi all Gmx usersI want to evaluate influence of pH on the stability of protein. can I use MD simulation for this goal? thanks Protonate the protein and any other relevant species in different forms characteristic of the dominant form at each given pH. The better way to do this is using constant-pH methods, such as those available in CHARMM. I believe there are implementations of this in GROMACS, but they are not natively supported. -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.
[gmx-users] evaluation of influence of pH on the stability of protein
On Monday, August 29, 2016 11:40 PM, Mahboobeh Eslamiwrote: Hi all Gmx usersI want to evaluate influence of pH on the stability of protein. can I use MD simulation for this goal? thanks -- 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.
[gmx-users] evaluation of influence of pH on the stability of protein
Hi all Gmx usersI want to evaluate influence of pH on the stability of protein. can I use MD simulation for this goal? thanks -- 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.