Re: [AMBER] PM6 charges for MD with AMBER

From: David Case <>
Date: Thu, 11 Jul 2019 13:39:37 +0000

On Thu, Jul 11, 2019, Thomas Evangelidis wrote:
>Maybe this is a recurrent question. I know there are better methods to
>optimize ligand geometry than AM1. For instance, I am using PM6. However,
>for the charge calculations, is the AM1 method with bcc corrections the
>recommended one? Can I replace it with the more rigorous PM6 or those
>charges would not be compatible with the GAFF2 force field?

The charge corrections applied in AM1-BCC assume that one is starting
with AM1 charges. As noted before, the initial derivation of these used
AM1-optimized geometries as well.

You are welcome to use a PM6-optimized geometry: just tell antechamber not
to minimize the input structure when computing AM1-BCC charges. I don't
think it is likely to generally be good to replace AM1 charges with PM6
charges, since the bond correction terms are designed to (partially) fix
the deficiencies of AM1 charges.


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Received on Thu Jul 11 2019 - 07:00:02 PDT
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