Re: [AMBER] pH based conformational study

From: Jason Swails <>
Date: Wed, 16 Jun 2010 09:19:32 -0400

On Wed, Jun 16, 2010 at 2:55 AM, Sangita Kachhap <>wrote:

> Hello all
> I am doing pH based conformational study.
> I have prepared CPIN file there is by default protonation state is 0 for
> side chain
> of titratable residues.During generation of this file I havent specify the
> protonation state.
> Should I modifify the protonation state before doing MD simulation or I can
> proceed,
> If is it so then why?
> Whatever I got from manual that during Md simulation diffrent ptonation
> state is
> sample out by each MC sampling step.
> So should I left initial protonation state 0 or chang it.
> Can anybody please explain this.

That is what I attempted to do with my previous email. It is unlikely that
you have to change it, and you may only have to if there are a couple of
carboxylates that are closely interacting (making it obvious that not both
can be charged). This may cause the system to blow up... but it's
unlikely. Just make sure that each time you restart a simulation, use the
cprestart generated in the previous step as the new cpin file. This will
make sure that you don't reset the resstate each time.

Good luck!

> With regard
> Sangita Kachhap
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Wed Jun 16 2010 - 06:30:06 PDT
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