Subject: Re: [charmm-bbs] Diazo dyes in CHARMM

From: Rick Venable <[email-masked]>
Date: Wed, 8 Nov 2000 13:20:12 -0500

See Alex MacKerell's web site at URL

	http://www.pharmacy.umaryland.edu/~alex/research.html

for information and references on the academic parameter development
process.

On Wed, 8 Nov 2000, Marcin Krol wrote:
> I want to simulate diazo dyes and their interactions with proteins in
> CHARMM using academic, all atom forcefield. I  built RTF file for my
> diazo dye and chose atom types that I thought fitted 'well' with my
> structure. However, I could not find proper atom types for sulphur in
> SO3H- and nitrogen in -N=N- and so on. Moreover, there were 'missing
> paramters'. So I used Quanta and got all atom types and
> missing paramters given by Parameter Chooser. However, these atom types
> and parameters belong to QUANTA_CHARMm forcefield.
> 
> Is it safe to take them to academic par22 FF? I'm afraid it isn't.

It may be or may not be safe, but it represents a significant change to
existing parameters and would require significant testing on model
compounds to verify or validate the changes.

> Maybe someone has parameters for diazo dyes in par22, or maybe someone can tell me how to transform
> parameters from CHARMm (Quanta) to CHARMM (academic)?
> How can I get parameters in another way?
> I know I'm asking a generic question, so I'd be also grateful if you
> could refer me to a good book/article about parametrization process for
> small ligand molecules.

--
Rick Venable                  =====\     |=|    "Eschew Obfuscation"
FDA/CBER Biophysics Lab       |____/     |=|
Bethesda, MD  U.S.A.          |   \    / |=|  ( Not an official statement or
[email-masked]          |    \  /  |=|    position of the FDA; for that,
[email-masked]              \/   |=|    see   http://www.fda.gov  )