AMBER Archive (2006)

Subject: Re: AMBER: Antechamber & atom types

From: David A. Case (
Date: Fri Apr 21 2006 - 10:22:45 CDT

On Thu, Apr 20, 2006, FyD wrote:

> I used two versions of antechamber: the version 1.25 from the antechamber web
> site and the version from amber8 (patches 3 6 and 8 applied). All the atom
> types were well assigned for all the structures. However, the two versions of
> antechamber do not find the same atom types for one type of hydrogen (h4 or ha)
> for one class of molecule:
> R ha|h4 (h4 is found by the version 1.25)
> C = C
> R Cl
> Which one is the right one ?

There are changes in gaff for amber9 and for version 1.25 that are not in
amber8. So my guess is that the "version 1.25" result is the more correct
one. But I have not studied this in any detail.

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