Re: AMBER: Residue question

From: David A. Case <>
Date: Wed, 10 Mar 2004 08:10:11 -0800

On Tue, Mar 09, 2004, wrote:
> When I define my own residues in leap, I have to define the atom type
> (e.g. h1, c3, hn, etc.). Do I also have to define the charge of the
> individual atoms? If so, where do I find the information on this to do it?

Charges for amber are generally determined by a RESP procedure. There
is a link on the Amber web page to help for this. You can also use the
AM1-BCC procedure; see the Antechamber chapter of the Users' Manual.

> On a different note, what is the difference between the nucleotides
> defined in the different libraries (e.g. DAN vs. DA)?

Please see p. 40 of the Amber 7 Users' Manual.

....good luck...dac
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Received on Wed Mar 10 2004 - 16:53:00 PST
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