AMBER Archive (2005)

Subject: AMBER: GB and mm_pbsa.pl

From: Nelson Fonseca (nfonseca_at_dq.ua.pt)
Date: Wed Apr 20 2005 - 06:48:48 CDT

Experience is what you get when you don't get what you
want.

                      -- Dan Stanford--

Dear list,

Im using mm_pbsa scripts to calculate binding energies
between a macrocycle with total charge +6 and some anions.
I have experimental constants of formation for the system.
these were derived in DMSO solution.

I have performed some MD runs and try to calculate the
binding energies form my simulations. I have noticed that
using AM1-BCC charges the free energy is overestimated
about 5 times. So I have changed to Gasteiger Charges and
the results were better but not excelent.

The important question is: can I calculate the solvation
free energy with GB method setting the value for the
deilectric cobstant equal to the experimental values for
DMSO? I can reach better results than using PB solver.
Does it make sense to use a GB model for non-aqueous
simulations? The true is that the results agree well with
the experimental usin GB instead of PB.

Could anyone point me to good references of the influence
of tha charge method in calculating free energies of
binding?

Thanks in advance

Nelson Fonseca
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