AMBER Archive (2008)

Subject: Re: AMBER: Tough time with antechamber

From: Junmei Wang (
Date: Thu Jan 24 2008 - 17:49:51 CST

It is a good idea to write out the optimized structure in pdb format when
the output format is -gout or divout or charge method is bcc or mul or cm1
or cm2. I would like to call it divcon.pdb and mopac.pdb.
But if the starting geometry is really bad, I suspect AM1 or PM3
optimization always produces sound structure.

In AMBER10, the newly introduced program, acdoctor can help users to detect
lots of input problem. For this particular case, acdoctor finds that there
are more than one unit (since HD is isolated from the other atoms) and
prints out an error message.


On Jan 24, 2008 12:42 PM, David A. Case <> wrote:

> 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.
> ...dac
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