These files are attached.
Thank you
Nan
On Fri, Jun 8, 2012 at 12:03 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Can you attach your mm_pbsa.pl and MMPBSA.py input files?
>
> Thanks,
> Jason
>
> On Fri, Jun 8, 2012 at 12:01 PM, Nan Li <nli4.ncsu.edu> wrote:
>
> > mm_pbsa.pl is from Amber11. I think there are not SCEE and SCNB in this
> > version, are there? Both tests are with GB=1.
> >
> > Has anyone else compare the results from these two scripts before?
> > Thanks a lot.
> >
> > Nan
> > On Thu, Jun 7, 2012 at 4:10 PM, Jason Swails <jason.swails.gmail.com>
> > wrote:
> >
> > > 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
> > > _______________________________________________
> > > 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Jun 08 2012 - 09:30:04 PDT
