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From: Soumendranath Bhakat <bhakatsoumendranath.gmail.com>

Date: Wed, 2 Jul 2014 16:32:03 +0200

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>
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*> 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
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*> > running 10 ns md simulation.
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*> > Since I don't need gb namelist, I have used this input file:
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*> >
*

*> >
*

*> >
*

*> >
*

*> >
*

*> >
*

*> >
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*> > *Input file for running PB and GB in serial&general startframe=1,
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*> > endframe=25000, keep_files=2,/&pb istrng=0.100, /*
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*> >
*

*> > Although I have checked the structure of the complex after production
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*> and I
*

*> > am sure about the binding of ligand to its proper site, ΔG value is
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*> > positive. Here is the end part of the FINAL_RESULT.dat file:
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*> >
*

*> >
*

*> >
*

*> >
*

*> > *Differences (Complex - Receptor - Ligand):Energy Component
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*> > Average Std. Dev. Std. Err. of
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*> >
*

*> Mean-------------------------------------------------------------------------------*
*

*> > *BOND 0.0000 0.0001
*

*> > 0.0000*
*

*> > *ANGLE 0.0000 0.0000
*

*> > 0.0000*
*

*> > *DIHED 0.1101 0.1072
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*> > 0.0024*
*

*> > *VDWAALS -51.3535 4.0635
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*> > 0.0908*
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*> > *EEL 106.0784 20.1745
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*> > 0.4510*
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*> > *1-4 VDW 0.0000 0.0001
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*> > 0.0000*
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*> > *1-4 EEL -0.0000 0.0001
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*> > 0.0000*
*

*> > *EPB -77.7007 17.4595
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*> > 0.3903*
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*> > *ENPOLAR -42.1622 2.6622
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*> > 0.0595*
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*> > *EDISPER 69.0762 4.0390
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*> > 0.0903*
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*> >
*

*> > *DELTA G gas 54.8350 20.3812
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*> > 0.4556*
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*> > *DELTA G solv -50.7868 17.6481
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*> > 0.3945*
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*> >
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*> > *DELTA TOTAL 4.0482 6.0860
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*> > 0.1361*
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*> >
*

*> >
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*> > 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
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*> binding free energies than the typical approach where the nonpolar energy
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*> is represented as a simple proportionality of the SASA.
*

*>
*

*> As the nonpolar contribution to binding is +27 kcal/mol (and typical
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*> contributions from the simple SASA model is more like 5 kcal/mol), this
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*> will certainly make your binding free energy negative. However, that
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*> doesn't necessarily mean that the absolute binding free energy is more
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*> reliable. MM PBSA calculations are more appropriate for relative binding
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*> free energies.
*

*>
*

*> HTH,
*

*> Jason
*

*>
*

*> --
*

*> Jason M. Swails
*

*> BioMaPS,
*

*> Rutgers University
*

*> Postdoctoral Researcher
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

Date: Wed, 2 Jul 2014 16:32:03 +0200

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:

-- Thanks & Regards; Soumendranath Bhakat _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Jul 02 2014 - 08:00:02 PDT

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