AMBER Archive (2002)

Subject: Re: several questions

From: Heather A Carlson (carlsonh_at_umich.edu)
Date: Tue Jul 23 2002 - 22:17:35 CDT

Hi All,

We've taken the time to carefully parameterize polyphosphates to allow
people to model ATP, ADP, GTP, etc with AMBER. We're writing up the
work now, and will be submitting the paper to J Comp Chem by the end
of the month. We're happy to share the parameters with others, but
we don't want to post them on a website in case that would count as
"previous publication."

Please feel free to contact me directly for these params.

Heather (carlsonh_at_umich.edu)

> > Is there a pre-defined residue type for FULL nucleotides, including
> > the tri-phosphate?
> > Is there a pre-defined triphospate defined as a residue in its own
> > right?
> > Is there some standard way to deal with this problem?
>
> You'd think there should be, and I keep hoping that people that have worked
> with di- and tri-phosphates would contribute to Richard Bryce's database
> (see the "contributed parameters" link on the Amber Web page). Maybe someone
> on the list will have parameters to share....

--------------------------------------------
Heather A. Carlson
John Gideon Searle Assistant Professor of Medicinal Chemistry
Assistant Professor of Chemistry
Affiliated Faculty, Biophysics Research Division
Affiliated Faculty, Bioinformatics and Computational Biology

University of Michigan, Ann Arbor
College of Pharmacy
428 Church St.
Ann Arbor, MI 48109-1065

Phone: (734) 615-6841
E-mail: carlsonh_at_umich.edu
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