On Tue, Apr 16, 2013 at 12:44 AM, James Starlight <jmsstarlight.gmail.com>wrote:
> Dear Dr. Case,
>
> thank you for your response! The main issue why I've decided to switch from
> sqm is that the topology with not integer charge was producing during
> parametrization of large ligand (~60 atoms). In my research I deal with the
> horomone-like ligands of membrane receptors. What method of charge
> computations would be best suitable for the parametrization of such
> molecules for amber force fields?
>
When you say 'non-integer', exactly what charge is coming out? Round-off
errors of 0.0001 to 0.001 are not unusual, and are small enough that you
can manually adjust the charges on one of the atoms to achieve neutrality.
sqm and mopac should give roughly the same results (exactly the same if
they use the same values for the fundamental constants -- I'm not sure
whether or not this is true).
If the assigned charges result in a significant non-integral charge, the
problem may lie with antechamber (in which case using mopac won't help),
and we should get that fixed.
All the best,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Apr 16 2013 - 05:00:05 PDT
