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
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> 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 - 12:30:04 PDT
