AMBER Archive (2008)

Subject: Re: AMBER: How to confirm atom types of small molecule perceived by antechamber

From: David A. Case (case_at_scripps.edu)
Date: Mon Jun 23 2008 - 09:56:17 CDT

On Mon, Jun 23, 2008, xiaonan zhang wrote:

> However, I am still nervous about the validity of the atom types and
> bond order assigned to the inhibitor.
> the prepin file have the atom types for every atom, but unfortunately I
> cannot understand it because there
> are no description about the naming conventions of these atom types in the
> manual.

See the gaff paper for details about atom types:

%A J. Wang
%A R.M. Wolf
%A J.W. Caldwell
%A P.A. Kollman
%A D.A. Case
%T Development and testing of a general Amber force field
%J J. Comput. Chem.
%V 25
%P 1157-1174
%D 2004

[This is the first reference in Chap. 4 of the AmberTools manual.]

....dac

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