AMBER Archive (2006)

Subject: Re: AMBER: MMPBSA: magnitude of PB calculation

From: Thomas Steinbrecher (steinbrt_at_scripps.edu)
Date: Mon Feb 06 2006 - 02:54:01 CST

Dear Sishi,

PB contributions that amount to hundreds of kcal per mole can be expected
for an MMPBSA calculation, however they should cancel out more or less in
the final deltaG. Check the individual breakdown of LIG REC and COM to see
where huge differences in PBCAL lie. It might be possible that something
in your calculation/assignment of charges does not work right.

If you placed a nonpolar ligand in a very polar binding site that is
otherwise solvent accessible, a huge positive contribution of solvation to
deltaG would be expected instead of the negative you got.

Regards,

Thomas

> > >I'm calculating the binding energy of a protein with a nonpolar ligand
> > using
> > >MMPBSA, the results that I obtained are as follows:
> > >
> > >ELE -27.41 3.62
> > >VDW -52.37 2.66
> > >INT 0.00 0.00
> > >GAS -79.78 4.73
> > >PBSUR -3.37 0.22
> > >PBCAL -573.75 28.49
> > >PBSOL -577.12 28.40
> > >PBELE -601.16 27.46
> > >PBTOT -656.90 26.82
> > >
> > >I also performed entropy calculation using nmode, which results in an
> > entropy
> > >contribution of around -5 kcal/mol (T=298) If that's the case, the overall
> > >absolute binding energy amounts to -650 kcal/mol,which is obviously
> > >non-physical. Is there any obvious anormaly in my PB results? Any
> > >suggestions/advice will be more than welcome.
> > >
> > >Thanks,
> > >Sishi.
> > >
> > >
> > >-----------------------------------------------------------------------
> > >The AMBER Mail Reflector
> > >To post, send mail to amber_at_scripps.edu
> > >To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> > >
> > >.
> > >
> > >
> > >
> >
> > --
> > ====================================================
> > Ray Luo, Ph.D.
> > Department of Molecular Biology and Biochemistry
> > University of California, Irvine, CA 92697-3900
> > Office: (949)824-9528 Lab: (949)824-9562
> > Fax: (949)824-8551 e-mail: rluo_at_uci.edu
> > Home page: http://rayl0.bio.uci.edu/rayl/
> > ====================================================
> >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu