Dear Jason,
Thank you very much for your message. I will follow as your suggestion.
Regards,
Xioling
> Date: Mon, 14 May 2012 01:11:19 -0700
> From: jason.swails.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] Large standard deviation of entropy obtained from NMODE
>
> 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
> >
> > _______________________________________________
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> > 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 Tue May 15 2012 - 19:00:03 PDT
