Re: [AMBER] constant pH equilibration confusion

From: Jason Swails <>
Date: Sat, 19 Jun 2010 11:49:15 -0400


The restraints for the constant pH simulations should not be any different
than restraints for any other simulations. What I normally do is just
restrain the backbone atoms (CA, N, C, and O). Since you should be using
SHAKE anyway, there's really no point in restraining hydrogen atoms I
wouldn't think. I've noticed that heating and equilibration has to be done
more carefully with constant pH simulations as opposed to other types of
simulations, so you should keep relatively strong restraints for heating (if
you're using ntr, use restraint_wt=5 or something to that effect). You can
then reduce these to ~1 for your equilibration (which is run AFTER heating,
it's not a part of heating).

If one of your steps generates a cprestrt file, you should use that as the
cpin file for the next simulation. The only real differences between the
cprestrt and cpin will be the resstate array. All other variables will be
the same, although the formatting will look drastically different.

The cprestrt file will hold the protonation states (resstate) for each of
your titratable residues that correspond to the conformation defined in your
restrt file.

Hope this helps,

On Sat, Jun 19, 2010 at 3:55 AM, Sangita Kachhap <>wrote:

> Hello all
> I am doing constant pH simulation using amber10.
> I have minimized it using restriant on all hydrogen and generated restrt
> file.
> Now I have to euqilibrat it with heating 0 - 300K.
> Should I use restraint at this time if yes then what I should consider for
> it ?
> Should I make restrt and cprestrt file during equilibration?
> As cprestrt contains protonation state definitions, final protonation states
> for restart (same format as cpin).
> Anybody please suggest me.
> 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 Sat Jun 19 2010 - 09:00:03 PDT
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