Re: AMBER: some questions and problems about antechamber and divcon

From: David A. Case <>
Date: Fri, 2 Jun 2006 17:12:42 -0700

On Fri, Jun 02, 2006, Zhihong Yu wrote:
> 2:I found out that no Cartesian coordinate is in prepi files, then what's
> difference exist in prepi and prepc ? which is better or both are equal ?

The "i" in prepi means that it uses internal coordinates. Generally, we
recommend that users avoid either of the prep file formats if possible, and
use the mol2 format instead. Mol2 is a much more widely accepted format, and
is what we generally use for small molecules.

> 3:Charges from gaussian and bcc calculation are different more or less,
> which is more preferalbe as your experience ?

RESP charges are probably broadly more useful in force field calculations than
are am1-bcc, but averages don't necessarily tell you anything about a
particular instance. The am1-bcc procedure is supposed to mimic RESP, so
where there are differences, it reflects a limitation of the am1-bcc approach.

...hope this helps...dac

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Received on Sun Jun 04 2006 - 06:07:18 PDT
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