AMBER Archive (2008)

Subject: Re: AMBER: Tough time with antechamber

From: David A. Case (
Date: Thu Jan 24 2008 - 12:42:56 CST

On Thu, Jan 24, 2008, David Mobley wrote:

> For the reason Junmei points out, I always prefer to use mol2 files as
> input to antechamber over pdb files. I often use the OpenEye tools
> (free to academics) for generating mol2 files from IUPAC names,
> crystal structures, etc.

This is a good point, but doesn't really invalidate the point the antechamber
can have problems when the input strutures are bad. (Junmei: we need to put
something in the Users' Manual about this.) I suspect that in many cases,
doing a simple geomtry optimization with AM1 or PM3 before giving the
structure to antechamber might be a real help. It might be worth having an
option in antechamber to do just that.

Also, the bcc charge procedure creates an AM1-optimized geometry, but then
discards it, and writes out the original geometry in the output files. Should
we change this behavior, or have a flag that could keep the optimized
geometry? At a minimum, it should be possible for the user to see what AM1
did to their structure.


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