Re: [AMBER] sqm x mopac in AmberTools 1.3

From: David A. Case <>
Date: Tue, 22 Dec 2009 22:50:35 -0500

On Tue, Dec 22, 2009, Alan wrote:
> Then I tested antechamber on a ligand with sqm and mopac (which I just
> copied mopac and from amber10/bin into amber11/bin):
> First: with mopac, I got things done in 1min 20 s, with sqm it did in 15m 20
> s. Yes, 14 min more!
> The results for partial charges were almost identical.

The new sqm program has *much* more stringent convergence criteria than did
the old mopac program, in an attempt to make am1-bcc charges more
reproducible. This can increase computation times, as you have found.

See note 6 on p. 82 of the Users' Manual for a discussion. If computation
time is a problem, you can loosen the SCF and geometry convergence criteria,
as discussed there.

> Mopac saves a file mopac.pdb which is an optimised structure. Does sqm do
> the same? How?

The final coordinates are in the sqm.out file. You could also uncomment
line 555 in amber11/src/antechamber/charge.c, to have antechamber write
the optimized coordinates as it has done with mopac.


AMBER mailing list
Received on Tue Dec 22 2009 - 20:00:04 PST
Custom Search