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
>
>
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>
--
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 - 20:00:02 PDT
