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
>>
>>
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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 - 20:00:03 PDT
