AMBER Archive (2005)

Subject: Re: AMBER: mm_pbsa

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Thu Nov 10 2005 - 08:08:24 CST

Hi Chen,

Have you tried using

set default pbradii mbondi2

in setting parameter/topology and crd files in leap.

Have you checked that your structure(s) converged well
during MD? How does the EPtot energy plot look for
your MD simulation?

Also, make sure that you used PB and GB parameters in
your mm-pbsa input as suggested in Hunter Gohlke's
papers..

In general, electrostatic contributions to the free
energy of solvation will differ between PB and GB
methods. This especially happens when internal H-bonds
are involved. That is, you may end up with getting
more negative energy values with the PB method
compared to the GB method in mm-pbsa computations.
Therefore, be cautious when comparing the PB and GB
results.

regards,

jenk.

--- Wei Chen <gtg553p_at_mail.gatech.edu> wrote:

> Hello, all Amber users,
>
> I am using mm_pbsa in Amber8 to calculate binding
> free energy of two-protein
> binding. When I used PB or GB to calculate polar
> solvation energy, I got very
> different values. The free energies (not including
> entropy) are 93.28+/-90.46
> kcal/mol with PB and -37.43+/-5.54 kcal/mol with GB.
> First of all, the mean
> value with PB is positive, which doesn't make any
> sense. And the standard
> deviation with PB is so large that it is the same
> order as the mean value. The
> value with GB seems to be more acceptable. However,
> I think that GB is an
> approximation to PB. So anybody can help me to
> understand the results?
>
> Thanks!
>
> Wei Chen
>
> --
>
>
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