Subject: CCL: SOMFA TF2 File Format Converter

From: "Axel Mathieu" <Axel.Mathieu<<at>>neokimia.com>
Date: Mon, 1 Dec 2003 10:10:30 -0500

Greetings CCL'ers,
I just came across SOMFA but unfortunately it works with its own TF2 file format. Did anybody script a file conversion tool for this file type?
APM

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From: David Gallagher <dgallagher<<at>>cachesoftware.com>
Date: Mon, 01 Dec 2003 10:45:01 -0800

Hi Martin,

I am not sure is this helps any, but you can calculate the partial charges 
on whole proteins (with or without solvation) using the linear scaling 
method in MOPAC 2002 with AM1, PM3, or PM5. If you compute the partial 
charges on a sequence of conformations, you could then plot the partial 
charge on any particular atoms as a function of geometry. Each SCF 
calculation would typically take from a few minutes to a few hours on a 
Windows desktop computer, and the whole process can be automated in CAChe.

Regards,
David Gallagher
CAChe Group, Fujitsu

At 05:17 PM 11/25/2003 +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.
>
>Thank you in advance
>marcin
>
>
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