On Tue, Dec 22, 2009, Alan wrote:
>
> Then I tested antechamber on a ligand with sqm and mopac (which I just
> copied mopac and mopac.sh 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.
...dac
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Received on Tue Dec 22 2009 - 20:00:04 PST
