AMBER Archive (2005)

Subject: CORRENDUM: Re: AMBER: mm_pbsa

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Sat Nov 12 2005 - 02:31:27 CST

Hi Chen,

I have just noticed that there is typo in my previous
E-Mail. The author of MM_PBSA paper is Holger Gohlke.
He has published two informative papers with Prof.
David Case regarding the MM-PBSA module of AMBER 8.
See Amber manual.

regards,

Jenk.

--- Cenk Andac <cenk_andac_at_yahoo.com> wrote:

> 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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>
>
>
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