[gmx-users] MD simulation with varying pH
gauravgoeluta at gmail.com
Thu Jul 5 09:29:17 CEST 2012
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.
On Thu, Jul 5, 2012 at 12:33 PM, J Peterson <think_beyond at aol.com> 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.
> 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 gmx-users at gromacs.org
> * 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 gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Gaurav Goel, PhD
Department of Chemical Engineering
Indian Institute of Technology, Delhi
Hauz Khas, New Delhi 110016
More information about the gromacs.org_gmx-users