In Amber11 the SCEE flag is not explicitly set in the nmode-input files
created
by mm_pbsa.pl, therefore the default value of SCEE=2.0 is used in the nmode
calculation, wherease for the minimization in Sander SCEE is set according to
the definition in the topology file (default 1.2). This was corrected in
Amber12.
Best regards,
Nadine
>
> 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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