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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Received on Tue May 29 2012 - 19:30:03 PDT
