The code has changed significantly enough that -rewrite-output will not
work on output from MMPBSA from AmberTools 1.5. The number of intermediate
files is significantly reduced and the names of the intermediate files that
get parsed are subtly different -- but this difference is enough so
MMPBSA.py from AmberTools 12 won't find the files it needs to parse.
All the best,
Jason
On Wed, May 30, 2012 at 5:11 AM, Cao Yang <muxiachuixue.163.com> wrote:
> 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
> >_______________________________________________
> >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 Wed May 30 2012 - 06:00:04 PDT
