Hi Jason,
I just installed AmberTools 12. When I try to re-run the decomposition analysis with the commad below:
mpirun -np 10 MMPBSA.py -O -i decomp.in -o FINAL_RESULTS_MMPBSA.dat -sp com_solv.prmtop -cp com_nosolv.prmtop -rp rec.prmtop -lp neg_gaussian_LUT.prmtop -y ../production2.mdcrd > progress.log 2>&1 -rewrite-output
MMPBSA.py failed with the following error:
Reading command-line arguments and input files...
MMPBSA_Error: _MMPBSA_info is needed for -rewrite-output!
Exiting. All files have been retained.
What does the _MMPBSA_info means here?
When I re-run the job with MMPBSA in AmberTools 1.5, the error does not occur.
Here is my input file:
Per-residue GB and PB decomposition
&general
startframe=201, verbose=1,
strip_mask=":WAT:Cl-:CIO:Cs+:IB:K+:Li+:Na+:Rb+"
/
&gb
igb=5, saltcon=0.100,
/
&pb
istrng=0.100,
/
&decomp
idecomp=1,
dec_verbose=1,
/
Thanks in advance!
Cao Yang,
Zhejiang University
At 2012-05-30 13:06:23,"Jason Swails" <jason.swails.gmail.com> wrote:
>Hi Cao,
>
>Here is a copy of the email I sent to your other post earlier today:
>
>I've already addressed the normal mode standard deviations in my response
>to the other thread (which you contributed to as well). The patch for that
>is attached to that response.
>
>Bill's email is correct about these issues being addressed in AmberTools
>12, so I will simply explain the large standard deviations for
>decomposition analysis in AmberTools 1.5 here. The large standard
>deviations (for the DELTA decomposed values only) result from how the std.
>devs are calculated.
>
>Regardless of whether a single or multiple trajectory protocol is used, the
>standard deviation is calculated by the square root of the sum of squares
>of the standard deviations of the complex, receptor, and ligand (that is,
>it's propagated as though the std. devs. of the different species are
>completely uncorrelated). This was done because it was determined that
>storing entire arrays of all terms for all snapshots could require too much
>memory (indeed, in one of our tests for pairwise decomposition we consumed
>> 8 GB of RAM). Therefore, we just keep a running sum and running sum
>squared for each term (so the test that used to take > 8 GB of RAM now
>takes ~512 MB of RAM instead). The way we parsed the file made another
>approach difficult to adopt.
>
>For single trajectories, though, snapshots are, more or less, perfectly
>correlated between the complex, receptor, and ligand (since the
>conformations are the same in each state). Therefore, the variance
>calculated as a sum-of-squares will drastically overestimate the variance
>calculated from a population of DELTAs (that is, calculating the standard
>deviation of the DELTA values for each snapshot).
>
>In AmberTools 12, the decomposition parser was completely rewritten so that
>we could keep a running sum and sum-of-squares of the DELTA values as well.
> This way, the memory requirements were kept at a minimum and we could
>provide more realistic values of the standard deviation for the DELTA
>section of the decomposition analysis.
>
>HTH,
>Jason
>
>On Tue, May 29, 2012 at 9:49 PM, Cao Yang <muxiachuixue.163.com> wrote:
>
>> 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
>> >> 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
>>
>
>
>
>--
>Jason M. Swails
>Quantum Theory Project,
>University of Florida
>Ph.D. Candidate
>352-392-4032
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>AMBER mailing list
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Received on Wed May 30 2012 - 05:30:03 PDT
