Subject: Re: CCL:Diazo dyes in CHARMM

From: Don Gregory <[email-masked]>
Date: Wed, 08 Nov 2000 12:44:33 -0800

Hi Marcin,
Your question is one that MSI often asked.
The essense of what you are asking, is "how transferrable are
these prameters (between the MSI/Quanta/CHARMm force-field
[Momany & Rone], and the academic CHARMM22 force-field)?"

Transferrability is a common, but I think poorly understood, concept
in empirical force-field usage.  In the most narrow sense, it is
meant to refer to the ability to optimize on small model compounds,
but then use the optimized parameters is other chemical species.
In this way, one can develop parameters by doing high-level QM
calculations on 'peptide-like' models, and the assumption/belief is
that these parameters will give reasonable results when used
to calculate protein characteristics.
This usage of 'transferrability' is one that I think is a reasonable one.

This concept can quite easily be extended, however, to the next
level, and that is your question here.
"Can parameters optimized for one force-field, be used in another
   force-field?"
The answer to that is ...... proceed with caution!

My advice is to look at the other parameters you will be using,
i.e. those that apply to the protein in this case, in both force-fields.
If they are not too dissimilar (you have to decide) then you may
feel comfortable with this level of approximation.

As always, of course, an explicit description of the origin of all
parameters used (even to the extent of saying 'from Quanta's
Parramater Chooser') is extremely importnant.

Hope this helps!
DG

At 06:01 PM 11/8/00 +0100, you wrote:
>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
>
>
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Dr. Don Gregory ([email-masked])
CHARMm Product Marketing Manager
Molecular Simulations Inc. (http://www.msi.com)
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San Diego, CA  92121
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