AMBER Archive (2009)

Subject: Re: [AMBER] antechamber am1-bcc issues

From: case (case_at_biomaps.rutgers.edu)
Date: Thu Aug 20 2009 - 06:18:52 CDT

On Wed, Aug 19, 2009, Khavrutskii, Ilja wrote:
> >
> > The exact command I used was:
> >
> > antechamber -i catechol.pdb -fi pdb -o oh2bnz.mol2 -fo mol2 -c bcc -s 2
> > -at gaff -ek "AM1 ANALYT GRAD LET GNORM=1.D-8 SCFCRT=1.D-6 XYZ"

It looks like the mopac6 compiled with gfortran (as in AmberTools 1.2)
does not respond well to the keywords you use above. It seems to run fine
with the default values (AM1 PRECISE), giving an optimized AM1 energy of
-66.31 (versus -66.46 for a more complete minimization we do with our
in-house codes, and with essentially the same Mulliken charges, diffs of
0.001 electron.)

Of course, you are welcome to use whatever mopac version you prefer (just
edit mopac.sh). We may try out f2c...I tried *lots* of combinations of
mopac sources (5, 6, 7, 509mn, etc.) and many compilers in trying to find a
version that would work. What we came up with has seemed to work well for
many molecules.

...dac

p.s.: if I add "PRECISE" to the keywords listed above, then the calculation
completes, giving the same Mulliken charges as the standard calculation,
but doesn't find as precise a minimum as you have requested.

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