AMBER Archive (2006)

Subject: Re: AMBER: Denaturing MD

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Thu Sep 14 2006 - 18:55:59 CDT

> Can I use Amber to simulate a process of protein
> denaturation from low cincentration of Urea to high
> concentration of urea?

yes.

> Can I use AMber to simulate a process in which protein
> moves in a specific salt and a specifc salt
> concentration?

yes.

However, my casual answer of "yes" hides many details and potential issues
to worry about as this approach is realized, most importantly to know what
has been done previously and what is the best approach, using AMBER, to
move forward. This includes serious issues of sampling and time scale,
force field choice for protein, salt and/or denaturant, simulation choices
(T/P coupling, electrostatics treatment, solvation treatment) and likely
this type of project would require considerable computational power.

Before you begin, there is a *vast* literature on protein folding, protein
unfolding, and effect of differing solvent environments, salt,
denaturants, etc. An incomplete set of authors that immediately bounce to
my mind include some of the AMBER developer's like Simmerling / Roitberg /
Duan / Luo and others I am missing to larger communities including Pande,
Daggett, Mark, van Gunsteren, Sansom, Wolynes, Onuchic, Brooks, and many
many others.

I would first suggest looking through the literature to see what has been
done and what is possible; a search at PubMed for "protein unfolding
molecular dynamics" returns 460 hits. "protein folding molecular dynamics"
returns 1180 hits. "denaturant molecular dynamics" returns 49 hits. In
the meantime, I would play with tutorials to get a better understanding of
how AMBER works.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu