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
> 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 29 2012 - 21:00:03 PDT
