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
>
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Received on Thu Jun 07 2012 - 12:30:04 PDT
