Re: AMBER: charges in PBSA calculation

From: David A. Case <>
Date: Sun, 19 Aug 2007 17:57:14 -0700

> On Aug 18, 2007, at 10:20 PM, Neha Gandhi wrote:
> >
> >I have been performing pbsa calculations for charge ligands like
> >glycosaminoglycans. But I the PBTOTAL is high negative (-1000 Kcal/
> >mol) which is not accurate.

How do you know that this is "not accurate"? Have you compared results from
Amber to other programs, such as Delphi or MEAD? A lot depends on how large
the net charge is. Also, it is easier to spot problems in the gas -> liquid
solvation energy than in total energies-- remember that the zero of energy in
molecular mechanics is rather arbitrary.

There may still be a problem with the code, but one would need more
information to be sure.


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Received on Wed Aug 22 2007 - 06:07:14 PDT
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