Hi Jason,
I am grateful that your patch did resolve the problem of high deviation on entropy value. Unfortunately, it does not apply to the case of decomposing calculation. I noticed that in Amber's tutorial
(
http://ambermd.org/tutorials/advanced/tutorial3/py_script/section6.htm), the deviation of every residue is very high too. So, is this reasonable or the problem will not occur in AmberTools 12 ?
Thanks.
Cao Yang,
Zhejiang University
At 2012-05-30 11:30:01,"Jason Swails" <jason.swails.gmail.com> wrote:
>How embarrassing. I've fixed the issue. Please reverse the original patch
>by using the command (if you already applied that patch):
>
>cd $AMBERHOME
>patch -p0 -N -R < std_dev.patch
>
>Then, apply the attached patch using the command:
>
>cd $AMBERHOME
>patch -p0 -N < std_dev2.patch
>cd AmberTools/src/mmpbsa_py && make install
>
>Then re-run with -rewrite-output.
>
>This is the output I now get with your _MMPBSA_*_nm.out files:
>
>ENTROPY RESULTS (HARMONIC APPROXIMATION) CALCULATED WITH NMODE:
>
>Complex:
>Entropy Term Average Std. Dev.
>-----------------------------------------------------------
>Translational: 16.7223 0.0000
>Rotational: 17.0094 0.0028
>Vibrational: 2452.2343 4.1753
>Total: 2485.9660 4.1757
>
>
>Receptor:
>Entropy Term Average Std. Dev.
>-----------------------------------------------------------
>Translational: 16.7119 0.0000
>Rotational: 16.9984 0.0026
>Vibrational: 2432.7994 3.1862
>Total: 2466.5098 3.1868
>
>
>Ligand:
>Entropy Term Average Std. Dev.
>-----------------------------------------------------------
>Translational: 12.7647 0.0000
>Rotational: 10.2737 0.0000
>Vibrational: 15.7722 0.0002
>Total: 38.8106 0.0002
>
>
>DELTA S total= -19.3544 +/- 3.3742
>
>Thanks!
>Jason
>
>On Tue, May 29, 2012 at 7:45 PM, Cao Yang <muxiachuixue.163.com> wrote:
>
>> the files are attached.
>> Thanks.
>>
>>
>>
>>
>> At 2012-05-30 10:34:23,"Jason Swails" <jason.swails.gmail.com> wrote:
>> >can you attach your final output file and your _MMPBSA_*nm.out files so I
>> >can take a look? I want to see if I can reproduce these issues.
>> >
>> >On Tue, May 29, 2012 at 7:07 PM, Cao Yang <muxiachuixue.163.com> wrote:
>> >
>> >> Hi Jason,
>> >>
>> >> Thanks for your reply. The patch didn't work in my case. The std. dev.
>> >> became larger when I fixed the bug with your patch and used
>> -rewrite-output
>> >> to re-run. Now I am trying to install AmberTools 12.
>> >>
>> >> Cao Yang,
>> >> Zhejiang University
>> >> At 2012-05-30 01:28:39,"Jason Swails" <jason.swails.gmail.com> wrote:
>> >> >I have looked into it, and found the problem. AmberTools 12 never had
>> >> this
>> >> >problem, since the statistics were completely redone in a
>> safer(/better)
>> >> >way.
>> >> >
>> >> >Please apply the attached patch from AMBERHOME using the commands:
>> >> >
>> >> >cd $AMBERHOME
>> >> >patch -p0 -N < std_dev.patch
>> >> >cd AmberTools/src/mmpbsa_py && make install
>> >> >
>> >> >Then you should be able to use -rewrite-output to get the correct
>> standard
>> >> >deviations. The bug was subtle enough such that the test case actually
>> >> >didn't catch it for me (a coincidence based on the number of frames
>> used
>> >> in
>> >> >the test).
>> >> >
>> >> >I suggest upgrading to AmberTools 12, although it is still slightly
>> >> >cumbersome to use AmberTools 12 with Amber 11 to perform decomposition
>> >> >analysis.
>> >> >
>> >> >Thanks for the report!
>> >> >Jason
>> >> >
>> >> >On Tue, May 29, 2012 at 6:42 AM, Jason Swails <jason.swails.gmail.com
>> >> >wrote:
>> >> >
>> >> >>
>> >> >>
>> >> >> On May 28, 2012, at 11:52 PM, "Cao Yang" <muxiachuixue.163.com>
>> wrote:
>> >> >>
>> >> >> > Hello Bill,
>> >> >> >
>> >> >> > I got the same problem . When I use AmberTools1.5(with .bugfix27),
>> the
>> >> >> Std. Dev. is very high. Dose AmberTool12 help in this case?
>> >> >>
>> >> >> Yes. I still have to look into why AmberTools 1.5 has such poor
>> standard
>> >> >> deviation estimates for the binding entropy. (indeed, there is a lot
>> I
>> >> need
>> >> >> to look into). However, AmberTools 12 handles statistics in a more
>> >> reliable
>> >> >> way, and I've already verified that this problem is fixed in that
>> >> version.
>> >> >>
>> >> >> Thanks!
>> >> >> Jason
>> >> >>
>> >> >> --
>> >> >> Jason M. Swails
>> >> >> Quantum Theory Project,
>> >> >> University of Florida
>> >> >> Ph.D. Candidate
>> >> >> 352-392-4032
>> >> >>
>> >> >
>> >> >
>> >> >
>> >> >--
>> >> >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
>> >>
>> >
>> >
>> >
>> >--
>> >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
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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 Tue May 29 2012 - 22:00:03 PDT
