Re: [AMBER] pH-dependent folding simulation

From: Adrian Roitberg <>
Date: Wed, 01 Jun 2011 18:36:35 +0200

look at manual (Amber 11 only!) for constant pH simulations.

There is no tutorial yet, but the test cases should guide you reasonably
well. Now, this is advanced stuff, so you need to feel really
comfortable with regular sander and MD simulations before trying
constant pH.


On 6/1/11 6:32 PM, George Tzotzos wrote:
> I'm dealing with a protein whose 12-residue carboxy end is an unstructured random coil at pH 7. This terminal end undergoes a transition to helical form at pH 4.5
> I was thinking of following an approach similar to tutorial 3 to predict the folding of the terminal oligopeptide, however I don't have any clear ideas on how to factor in pH effects.
> I'd appreciate any ideas on this.
> Regards
> George
> _______________________________________________
> AMBER mailing list

                            Dr. Adrian E. Roitberg
                              Associate Professor
                Quantum Theory Project, Department of Chemistry
                            University of Florida
on Sabbatical in Barcelona until August 2011.
AMBER mailing list
Received on Wed Jun 01 2011 - 10:00:04 PDT
Custom Search