Hello,
Sorry it took so long for me to get to this. I have a couple comments.
First, I think this bug was fixed via bugfix.27 for AmberTools 1.5. In any
case, I suggest upgrading to AmberTools 12, since the script has been
updated, and I can verify with this updated version that your issue no
longer exists.
When I use the new version on the output files you provided, I get this
output:
Complex:
Entropy Term Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
Translational 15.4755 0.0000
0.0000
Rotational 14.9945 0.0167
0.0075
Vibrational 487.4325 1.9231
0.8600
Total 517.9026 1.9397
0.8675
Receptor:
Entropy Term Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
Translational 14.8601 0.0000
0.0000
Rotational 14.2156 0.0067
0.0030
Vibrational 247.0084 0.7832
0.3503
Total 276.0839 0.7900
0.3533
Ligand:
Entropy Term Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
Translational 14.8601 0.0000
0.0000
Rotational 14.2318 0.0116
0.0052
Vibrational 246.9027 0.5159
0.2307
Total 275.9945 0.5274
0.2359
Differences (Complex - Receptor - Ligand):
Entropy Term Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
Translational -14.2447 0.0000
0.0000
Rotational -13.4528 0.0234
0.0105
Vibrational -6.4786 2.5576
1.1438
DELTA S total= -34.1758 2.5798
1.1537
As expected, the standard deviation is significantly reduced (down to what
it should be) -- and this new version gives you the standard error of the
mean as well.
An additional comment about why the numbers do not exactly match your
values: The standard deviation in MMPBSA.py is actually calculated as the
square root of the variance. The difference between your values and the
values MMPBSA.py prints is the difference between the standard deviation of
the sample (MMPBSA.py) and the sample standard deviation (your values)
described here: http://en.wikipedia.org/wiki/Standard_deviation#Estimation
HTH,
Jason
P.S. -- You should be able to patch AmberTools 1.5 with bugfix.27 (I
suggest applying all bugfixes), rebuild MMPBSA.py (cd
$AMBERHOME/AmberTools/src/mmpbsa_py && make) and then just run the command
MMPBSA [original command-line arguments] -rewrite-output
to avoid redoing the calculation from the beginning (assuming, of course,
that you kept the necessary files to do so). If you still have problems,
please let me know.
On Sat, May 12, 2012 at 9:40 PM, Xioling Chuang <xioling_c.hotmail.com>wrote:
>
> Dear Experts,
>
> I tried to calculate the entropy for 5 snapshorts of DNA duplex using
> NMODE (MMPBSA.py).
> The result (file "FINAL_RESULTS_MMPBSA.dat") showed the total entropy (at
> 298.15 K) as following:
> => Complex: 517.90 +/- 1.94
> => Receptor: 276.08 +/- 0.79
> => Ligand: 275.99 +/- 0.53
>
> => delta S total: -34.18 +/- 18.89
>
> However, when I analyzed the average values and there standard deviations
> of the files
> "_MMPBSA_complex_nm.out" , "_MMPBSA_receptor_nm.out" and
> "_MMPBSA_ligand_nm.out", I got same average values but different S.D.;
> => Complex: 517.90 +/- 2.17
> => Receptor: 276.08 +/- 0.88
> => Ligand: 275.99 +/- 0.59
>
> => delta S total: -34.18 +/- 2.88
>
> As you can see, the S.D. of delta S total is very different compared with
> that obtained from file "FINAL_RESULTS_MMPBSA.dat".
> Please see attached files for *nm.out files.
>
> Could anyone give me the comment please?
>
> Regards,
> Xioling
>
> _______________________________________________
> 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 Mon May 14 2012 - 01:30:03 PDT
