AMBER Archive (2003)

Subject: Re: AMBER: charge definition

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Sat Sep 06 2003 - 14:00:01 CDT

Khanh KIm Dao wrote:
>
> Dear Amber users and other modeling experts,
>
> I use Amber7 and xleap to load a pdb file of a protein in complex with
> cAMP. But I got problem because xleap does not recognize the cyclic AMP
> molecule. From the Amber's users manual, I should create a prep file to
> define atom type and charge for this molecule. I suppose I can combine
> parameters from database for adenine and for phosphate group to define atom
> type. But how can I get define charge for cAMP?

Unless somebody can provide charges for cAMP, you need to calculate them
using either the "HF/6-31G* RESP" methodology or AM1-BCC. Starting
points in this direction (also with respect to references) are the
documentation for antechamber and resp in the amber manual as well as
appendix D. Also see the resp FAQ on the amber webpage:
http://amber.scripps.edu/Questions/resp.html.

Best regards

Holger

>
> Thanks for any suggestion,
> Dao
>
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-- 
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla, CA 92037   USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
email: gohlke_at_scripps.edu
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