AMBER Archive (2005)

Subject: Re: AMBER: mm_pbsa

From: Wei Chen (gtg553p_at_mail.gatech.edu)
Date: Fri Nov 11 2005 - 11:05:40 CST


Hello Jenk,

Thank you for your replies!

I run the equilibration with explicit water for 5 ns. Then I extracted 150
snapshots from the last 3ns. I didn't use "set default pbradii mbondi2" for the
simulation. Does it matter?

Actually, I used everything in the "Example" fold when I used MM/PBSA in
AMBER8. Do you think I need change somthing?

The parameters for PB are as follows:

#
PROC 2
REFE 0
INDI 1.0
EXDI 80.0
SCALE 1.5
LINIT 500
PRBRAD 1.6
#
RADIOPT 1
#
FOCUS 0
PERFIL 80.0
CHARGE ../my_amber94_delphi.crg
SIZE ../my_parse_delphi.siz
#
SURFTEN 0.005
SURFOFF 0.0
#

And the parameters for GB are as follows:

IGB 2
GBSA 1
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
#
SURFTEN 0.0072
SURFOFF 0.00

Do you have any suggestion?

Thanks!

Wei Chen

Quoting Cenk Andac <cenk_andac_at_yahoo.com>:

> 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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