Re: [AMBER] Antechamber/SQM

From: David A Case <>
Date: Tue, 11 Oct 2011 13:18:54 -0400

On Tue, Oct 11, 2011, Chidambar Kulkarni wrote:

> I wanted to know what is the maximum number of
> atoms that can be handled using ANTECHAMBER and SQM. I am asking this
> question because, I have systems consisting of more than 300 atoms or so and
> moreover I would not successfully create .mol2 file for a system containing
> 192 atoms. Any suggestions on how to handle this will be appreciated.

There is no fixed maximum number. The sqm program is used to compute am1-bcc
charges; if you have another way of getting charges for your system, then you
don't need to use sqm at all.

The am1-bcc procedure, by construction, tries to get an am1-optimized geometry
for your molecule. This can fail if the SCF fails to converge, or if the
geometry optimization fails to converge. Both are increasingly likely as the
number of atoms grows.

The whole design idea for gaff and am1-bcc was to get automated initial
guesses for charge and force field models for molecules likely to be
considered as inhibitors or ligands to proteins. Larger molecules (and
300 atoms certainly qualifies), can general be broken into smaller
fragments, for which force field models can be derived, then reassembled
to make models for the original, larger system. I hope you can see a way
to make such a strategy work for your systems.

...hope this helps...dac

AMBER mailing list
Received on Tue Oct 11 2011 - 10:30:03 PDT
Custom Search