Thanks a lot, David. I will do what you suggest and
post my conclusion here.
--- "David A. Case" <case.scripps.edu> wrote:
> 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
> well.
>
> 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.
>
> ...regards...dac
>
>
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Received on Thu Dec 16 2004 - 22:53:00 PST
