Dear Peterson, There's no magic wand for this. You'll need to find out pKa values of titrable amino acids in your protein (in literature, MEAD software, etc.). Then, you can protonate (pH<pKa) / deprotonate (pH>pKa) those group according to the pH.
-G On Thu, Jul 5, 2012 at 12:33 PM, J Peterson <[email protected]> wrote: > Dear GROMACS Users, > > I'm planning to work on a protein that activates itself under lower pH > conditions. And I don't have any clues how to do it in GROMACS. My first > question is about the possibilities to do this in GROMACS, has anyone done > this before? It can even be a constant simulations at a particular > lower/higher pH or gradually lowering/increasing pH. > > Any suggestion on this would give me a lead. > > Thanks > > Peterson J > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/MD-simulation-with-varying-pH-tp4999095.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Gaurav Goel, PhD Assistant Professor Department of Chemical Engineering Indian Institute of Technology, Delhi Hauz Khas, New Delhi 110016 India -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
