Thanks Justin for the information. But I had a further question regarding the simulation-if the active monomer exists only in the acidic pH, then will carrying out a simulation of the monomer with a drug at neutral pH help? regards, Anu George
----- Original Message ----- From: "Justin Lemkul" <jalem...@vt.edu> To: gmx-us...@gromacs.org Sent: Wednesday, May 3, 2017 5:37:33 PM Subject: Re: [gmx-users] MD at different pH On 5/2/17 11:31 PM, Anu George wrote: > Dear Gromacs users, > I am working on a tetramer(human beta-2 tryptase) protein which exist as an > active monomer at an acidic pH of about 6..If I have to do a molecular > dynamic simulation of the monomer with a small molecule, should the > simulation be carried out at this pH ? what are the steps I should follow? Calculate the pKa values for titratable residues and select their dominant protonation states at that pH when running pdb2gmx. -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. -- 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.
