Subject: Diazo dyes in CHARMM

From: Marcin Krol <[email-masked]>
Date: Wed, 8 Nov 2000 18:01:42 +0100 (MET)

Dear CCLers,
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.
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.
Thanks in advance
Marcin Krol