Dear Jason;
Will you please cite any paper which said that MM/PBSa protocol is better
than GBSA. Though I got numerous examples of GBSA better than PBSA e.g.
http://pubs.acs.org/doi/abs/10.1021/ci100275a
On Wed, Jul 2, 2014 at 4:13 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
>
> > On Jul 2, 2014, at 3:08 AM, Zeinab Tavasoli <zeinabtavasoli.gmail.com>
> wrote:
> >
> > Dear Users'
> >
> > I am performing free energy calculation with MM-PBSA.py for a crystal
> > structure of a protein-ligand complex.I have used MM-PBSA module after
> > running 10 ns md simulation.
> > Since I don't need gb namelist, I have used this input file:
> >
> >
> >
> >
> >
> >
> >
> > *Input file for running PB and GB in serial&general startframe=1,
> > endframe=25000, keep_files=2,/&pb istrng=0.100, /*
> >
> > Although I have checked the structure of the complex after production
> and I
> > am sure about the binding of ligand to its proper site, ΔG value is
> > positive. Here is the end part of the FINAL_RESULT.dat file:
> >
> >
> >
> >
> > *Differences (Complex - Receptor - Ligand):Energy Component
> > Average Std. Dev. Std. Err. of
> >
> Mean-------------------------------------------------------------------------------*
> > *BOND 0.0000 0.0001
> > 0.0000*
> > *ANGLE 0.0000 0.0000
> > 0.0000*
> > *DIHED 0.1101 0.1072
> > 0.0024*
> > *VDWAALS -51.3535 4.0635
> > 0.0908*
> > *EEL 106.0784 20.1745
> > 0.4510*
> > *1-4 VDW 0.0000 0.0001
> > 0.0000*
> > *1-4 EEL -0.0000 0.0001
> > 0.0000*
> > *EPB -77.7007 17.4595
> > 0.3903*
> > *ENPOLAR -42.1622 2.6622
> > 0.0595*
> > *EDISPER 69.0762 4.0390
> > 0.0903*
> >
> > *DELTA G gas 54.8350 20.3812
> > 0.4556*
> > *DELTA G solv -50.7868 17.6481
> > 0.3945*
> >
> > *DELTA TOTAL 4.0482 6.0860
> > 0.1361*
> >
> >
> > I don't know where to look for the origin of this problem
>
> Another thing to look at is the nonpolar solvation free energy method you
> are using. The default value for PB calculations tends to give much higher
> binding free energies than the typical approach where the nonpolar energy
> is represented as a simple proportionality of the SASA.
>
> As the nonpolar contribution to binding is +27 kcal/mol (and typical
> contributions from the simple SASA model is more like 5 kcal/mol), this
> will certainly make your binding free energy negative. However, that
> doesn't necessarily mean that the absolute binding free energy is more
> reliable. MM PBSA calculations are more appropriate for relative binding
> free energies.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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>
--
Thanks & Regards;
Soumendranath Bhakat
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Received on Wed Jul 02 2014 - 08:00:02 PDT
