AMBER Archive (2008)

Subject: Re: AMBER: Restraintmask and Restraint_WT : Question

From: Thomas Steinbrecher (steinbrt_at_scripps.edu)
Date: Fri Apr 04 2008 - 11:18:17 CDT

Hi Deepa,

there is no reason I am aware of why 100 kcal/molA^2 restraints should be
necessary for any type of simulation. 2-5 kcal/molA^2 works fine for all
cases I ever studied to keep proteins very close to there native structure
while water relaxes around them. In line with the philosophy of adding as
little non-physical terms to your simulation potential as possible, I
would set restraints to as weak as you can get away with.

I dont think it is necessary to have an additional minimization step in
which your protein relaxes and waters&ions are restrained. Just start your
equilibration process with the preminimized structure and keep restraints
on the protein until you have a reasonable system density and temperature.

Regards,

Thomas

Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA

On Fri, 4 Apr 2008, dpandit_at_brandeis.edu wrote:

> Hi:
> After going through tutorials on the amber website, I am aware that it is
> important not to set Restraint_WT too high. I have set Restraint_WT of 100
> kcal/Mol - A2 for protein during minimization allowing solvent and ions to
> move. However, I am not sure what is reasonable Restraint_WT if I want to
> keep solvent and ions restrained and let protein move or is it better to skip
> this step and do whole system minimization.
>
> Thanks,
> Deepa
>
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu