Re: AMBER: antechamber/Mopac: strange GTP charges

From: <>
Date: Thu, 13 May 2004 14:40:03 -0400

> I generated parameters for GTP with:
> But unfortunately the charges don't really make
> sense (not to me at least). Furthermore the charges are
> very different between the mopac output and the prep/pdb.
> Have a look at the phosphates (equivalent atoms get diff
> charges, oxygen with positive charge, P with -1.0000)

Hi Raik,

Our phosphate "tails" that we parameterized to make
ADP and ATP can also be used to create GDP and GTP.
It took a lot of work to get the charges, but more
importantly, the torsional terms in the polyphosphate
balance the huge internal electrostatics. If you use
the default-guess torsions, you will won't get the
right conformational behavior. We even had to create
a new atom type to specify the different behavior of
the terminal gamma-phosphate oxygens from the alpha-
and beta-phosphate oxygens.

I've asked my student to deposit her GDP and GTP
files to the contributed parameters list (the ATP
and ADP parameters are already there). In the
meantime, you can get them from Kristin by e-mail

Best of luck!! Heather
"Black holes are where God divided by zero" Steven Wright

Heather A. Carlson, Ph.D.
John Gideon Searle Assistant Professor of Medicinal Chemistry

University of Michigan Phone: (734) 615-6841
College of Pharmacy (2555 CCL) FAX: (734) 763-2022
428 Church Street E-mail:
Ann Arbor, MI 48109-1065
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Received on Thu May 13 2004 - 19:53:00 PDT
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