What version of Amber is mm_pbsa.pl from?
Also note any differences in the potential. Things to look out for in
particular -- what is SCEE and SCNB in the mm_pbsa.pl input file? Are you
running the MMPBSA.py test with a generalized born implicit solvent model
or not?
Also, MMPBSA.py uses the XMIN minimizer (mm_pbsa.pl uses the conjugate
gradient method in sander unless I'm mistaken). This means that the normal
modes were ultimately calculated for different structures for
mm_pbsa.pland MMPBSA.py. I think the XMIN minimizer is generally the
preferred
method for finding minima.
There are a lot of factors that could lead to differences, but I'm not sure
how sensitive the results would be to these. My guess is that if any of
them are most important, it's the minimization differences.
HTH,
Jason
On Thu, Jun 7, 2012 at 3:09 PM, Nan Li <nli4.ncsu.edu> wrote:
> Jason,
> Thank you for your reply.
> MMPBSA.py is from Ambertools 12.
>
> Nan
>
> On Thu, Jun 7, 2012 at 3:06 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
> > What version of MMPBSA.py are you using? If AmberTools 1.5, have you
> > applied all bug fixes? (Particularly, bugfix.27 and bugfix.28). If you
> > haven't, you should be able to use the "-rewrite-output" flag to avoid
> > redoing the calculation.
> >
> > HTH,
> > Jason
> >
> > On Thu, Jun 7, 2012 at 2:57 PM, Nan Li <nli4.ncsu.edu> wrote:
> >
> > > Dear all,
> > >
> > > I calculated the entropy for a peptide+watershell system by using both
> > > MMPBSA.py and MM_PBSA.pl.
> > >
> > > Peptide+watershell :complex; peptide :ligand
> > >
> > > Results for entropy that I got from these two scripts are different,
> > > especially for the receptor (watershell) :
> > >
> > > MMPBSA.py::
> > >
> > > ENTROPY RESULTS (HARMONIC APPROXIMATION) CALCULATED WITH NMODE:
> > >
> > > Complex:
> > >
> > > Entropy Term Average Std. Dev. Std. Err.
> of
> > > Mean
> > >
> > >
> > >
> >
> -------------------------------------------------------------------------------
> > >
> > > Translational 15.7572 0.0000
> > > 0.0000
> > >
> > > Rotational 15.4116 0.0127
> > > 0.0073
> > >
> > > Vibrational 1128.9861 13.2411
> > > 7.6448
> > >
> > > Total 1160.1549 13.2525
> > > 7.6513
> > >
> > >
> > >
> > > Receptor:
> > >
> > > Entropy Term Average Std. Dev. Std. Err.
> of
> > > Mean
> > >
> > >
> > >
> >
> -------------------------------------------------------------------------------
> > >
> > > Translational 13.7862 0.0000
> > > 0.0000
> > >
> > > Rotational 14.2357 0.1439
> > > 0.0831
> > >
> > > Vibrational 669.3464 47.3527
> > > 27.3391
> > >
> > > Total 697.3683 47.2087
> > > 27.2559
> > >
> > >
> > >
> > > Ligand:
> > >
> > > Entropy Term Average Std. Dev. Std. Err.
> of
> > > Mean
> > >
> > >
> > >
> >
> -------------------------------------------------------------------------------
> > >
> > > Translational 15.6553 0.0000
> > > 0.0000
> > >
> > > Rotational 15.2580 0.0166
> > > 0.0096
> > >
> > > Vibrational 732.7309 2.8869
> > > 1.6667
> > >
> > > Total 763.6439 2.9028
> > > 1.6759
> > >
> > >
> > >
> > > Differences (Complex - Receptor - Ligand):
> > >
> > > Entropy Term Average Std. Dev. Std. Err.
> of
> > > Mean
> > >
> > >
> > >
> >
> -------------------------------------------------------------------------------
> > >
> > > Translational -13.6842 0.0000
> > > 0.0000
> > >
> > > Rotational -14.0821 0.1415
> > > 0.0817
> > >
> > > Vibrational -273.0911 57.6574
> > > 33.2885
> > >
> > >
> > >
> > > DELTA S total= -300.8573 57.5159
> > > 33.2068
> > >
> > >
> > >
> > >
> > >
> > > MM_PBSA.pl::
> > >
> > > # COMPLEX RECEPTOR
> > > LIGAND
> > >
> > >
> > > # ----------------------- -----------------------
> > > -----------------------
> > >
> > > # MEAN STD MEAN STD MEAN
> > > STD
> > >
> > > # ======================= =======================
> > > =======================
> > >
> > > TSTRA 15.85 0.00 13.87 0.00 15.75
> > > 0.00
> > >
> > > TSROT 15.64 0.01 13.83 0.06 15.51
> > > 0.01
> > >
> > > TSVIB 1017.93 14.25 323.39 18.15 757.42
> > > 2.50
> > >
> > > TSTOT 1049.43 14.26 351.10 18.12 788.69
> > > 2.50
> > >
> > >
> > >
> > > # DELTA
> > >
> > > # -----------------------
> > >
> > > # MEAN STD
> > >
> > > # =======================
> > >
> > > TSTRA -13.77 0.00
> > >
> > > TSROT -13.70 0.05
> > >
> > > TSVIB -62.88 25.46
> > >
> > > TSTOT -90.35 25.42
> > >
> > > As shown above, the number for the vibration part of entropy from the
> > > Python script is twice as that from the perl script.
> > >
> > > Has anyone compare the results from these two scripts before? Any
> comment
> > > is welcome.
> > >
> > > Thank you.
> > >
> > > Nan
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Jun 07 2012 - 13:30:03 PDT
