Subject: Re: CCL:Polarization in proteins

From: Anton Feenstra <feenstra/at/chem.vu.nl>
Date: Wed, 26 Nov 2003 08:23:34 +0100

Marcin Krol wrote:

> Dear All,
> 
> I am interested in calculating polarization effects (changes in partial
> charges) on conformational changes in proteins. I know that there are
> many potentials for polarizable water (and other small molecules) models
> but I am looking for a (preferably free) program/forcefield that uses
> electonegativity equalization method and is parametrized for proteins.
> I would also be grateful for any links to relevant papers.

I would be very surprised indeed if such a parameterization exists, and
by the same token very much interested in seein it, too!

AFAIK there are only partially functional implementations for polarization
of large molecules in the mainstream simulation software. As for the water
models, from what I've heard about that up to now there are still so many
(new) questions to answer and issues to adress even for only water, that I
don't see people moving on to parametrizing polarizable protein forcefields
any time soon. Furthermore, there is still so much to be done on the
'classical' protein forcefields themselves!

-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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