Re: AMBER: About MM/PBSA, PB Calculation

From: David A. Case <>
Date: Thu, 16 Dec 2004 09:38:32 -0800

On Wed, Dec 15, 2004, nlxc wrote:
> I am trying to validate my MM/PBSA protocol and AM1-BCC charge by
> calculating the hydration energy of about 400 small compounds. Generally the
> correlation is ok, but those high polar ones have large errors. The energy
> difference between experiment data and my results of some compounds are as
> large as 10-15 Kcal. My calculated results for most of the compounds shift
> to the more negative region comparing with experiment data. I use Delphi for
> PB calculation. Ligand charges from AM1-BCC has been added into Delphi input
> file.
> 1) I found almost all of those compounds with large error are compounds with
> amine group (NH2 in the terminal.) or group O-C=O or group H-C=O Almost all
> the compounds with the above groups are not calculated very well.

This is useful information. Two things might be happening. First, it is
possible that antechamber is not giving the "correct" AM1-BCC charges. You
should see what you get for a few cases with RESP, and check the original
papers to see if the bond-charge increments are really being done correctly.
Second, it may be that one would need to define some new corrections for
certain types of functional groups. Again, comparing to RESP charges would
probably help. You could look at other force fields (especially OPLS or MMFF)
to see how these groups are handled there -- that might give some clues as

I hope you will report your conclusions here. There is no reason to think
that the current antechamber/gaff scheme should work equally well on all
compounds. But we can work to systematically improve it once we know where
the problems are.


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Received on Thu Dec 16 2004 - 17:53:00 PST
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