Through the simulation, I am trying to find out if the binding free energy of the drug-protein complex is strong enough for the drug to be a good inhibitor of the protein. so, does the pH of the simulation matter as in reality the active monomer exists in acidic pH conditions? Thanks Anu George
----- Original Message ----- From: "Justin Lemkul" <[email protected]> To: [email protected] Sent: Wednesday, May 3, 2017 8:15:33 PM Subject: Re: [gmx-users] MD at different pH On 5/3/17 10:04 AM, Anu George wrote: > 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? That depends on what your scientific goals/questions are and what you are actually trying to model. -Justin > regards, > Anu George > > ----- Original Message ----- > From: "Justin Lemkul" <[email protected]> > To: [email protected] > 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 [email protected] | (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 [email protected]. -- 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 [email protected].
