Hi Kenneth,
thanks again for suggestions! Also I'd be very thankful for any
contributions in the adjacent mmgbsa decomposition topic where I asked
about possible algorithm for the analysis and ranking of several
decomposition output to rank residues for each system according to the
decomposition total score. Here the idea that I define some threshold and
scan all strings (Residues) from the final_decompos_output.dat file. So If
residue has total score (in fact I don't know here what value should I take
into account assuming that I make my output using verbose=0 option) higher
than this threshold - I copy the string to some new txt file called
decompose_top.txt. Eventually I repeat this in loop for each of my
output.dat files obtaining equal number of new output files for the same
systems with 10-15 top residues-contributors. Does this approach is good in
general or there are better alternatives to rank decomposition outputs?
James
2015-02-03 20:24 GMT+01:00 Kenneth Huang <kennethneltharion.gmail.com>:
> James,
>
> Oh sorry, I completely missed the entropy part in your initial script. I
> was just talking about running a decomp from your GBSA output files, at
> which point I'd just restart the calculation.
>
> So my understanding of how it might work in principle is very hazy, but if
> what you're asking about is decomposing the entropy from GBSA per residue
> contribution, I think that's possible, with each residue giving you a
> summed value over the whole complex with it's contribution via entropy to
> the binding energy, or something along those lines.
>
> I think the file in nmode (AmberTools14/src/nmode/decomp.f90) is meant just
> for this sort of thing - that said, I've never tried using it or any of the
> above before, though, so I have no idea how much use/sense the results
> make. Assuming that's what you're asking about, and I didn't completely
> miss your question.
>
> Best,
>
> Kenneth
>
> On Tue, Feb 3, 2015 at 10:38 AM, James Starlight <jmsstarlight.gmail.com>
> wrote:
>
> > Hi Kenneth,
> >
> > How do you think is it reasonable to include entropy term in the
> > decomposition? I'm not sure how it would be possible in principle to
> > decompose entropy for each residue.
> >
> > James
> >
> > 2015-02-03 16:22 GMT+01:00 Kenneth Huang <kennethneltharion.gmail.com>:
> >
> > > That should fix the problem- I've run into an identical or very similar
> > > problem before, and from what you've said about the rest of the
> > calculation
> > > running fine, that's the only issue I can see in your decomp section.
> > >
> > > On the second point, I don't think you can run decomp on from a
> completed
> > > MMPBSA run, since I imagine the outputs from GB/PB might not be enough
> to
> > > provide the decomp info? That's purely speculative, so someone more
> > > knowledgeable might want to weigh in. As an aside, running very short
> > test
> > > runs of MMPBSA, ie 1-10 frames, to make sure there's no problem in your
> > > input script is a helpful way of not having to rerun an entire
> > calculation
> > > all over again.
> > >
> > > Best,
> > >
> > > Kenneth
> > >
> > > On Tue, Feb 3, 2015 at 3:09 AM, James Starlight <
> jmsstarlight.gmail.com>
> > > wrote:
> > >
> > > > Just noticed in the input file absence ob the "," after selection of
> > the
> > > > residues which was copied from the tutorial page exactly in this
> form.
> > > >
> > > > &decomp
> > > >
> > > > idecomp=1, print_res="1-289"
> > > >
> > > > dec_verbose=1,
> > > >
> > > >
> > > > Might it be the sourse of the problem? BTW Could I make decomposition
> > > based
> > > > on the finished mmgbsa analysis for particular system or
> alternatively
> > I
> > > > should to restart this calculations from the beginning?
> > > >
> > > >
> > > > James
> > > >
> > > > 2015-02-02 13:26 GMT+01:00 James Starlight <jmsstarlight.gmail.com>:
> > > >
> > > > > Dear Amber Users!
> > > > >
> > > > > I've faced with the problem during the residue decomposition
> > > calculations
> > > > > during the MMGBSA run. Here is my input made in accordance with
> the
> > > > > tutorial
> > > > >
> > > > > &general
> > > > >
> > > > > startframe= 1, interval=50, keep_files=2,
> > > > > strip_mask=:WAT:Cl-:NA+:K+:PPC, netcdf=1
> > > > >
> > > > > /
> > > > >
> > > > > &gb
> > > > >
> > > > > igb=5, saltcon=0.150,
> > > > >
> > > > > /
> > > > >
> > > > > &nmode
> > > > >
> > > > > nmstartframe=1, nminterval=1, maxcyc=10000, nmode_igb=1,
> > > > nmode_istrng=0.15,
> > > > >
> > > > > /
> > > > >
> > > > > &decomp
> > > > >
> > > > > idecomp=1, print_res="1-289"
> > > > >
> > > > > dec_verbose=1,
> > > > >
> > > > > In general I've obtained good values for dG including both enthalpy
> > and
> > > > > entropy terms. However decomposition output.dat file consisted of
> > only:
> > > > >
> > > > > | Run on Mon Feb 2 10:43:49 2015
> > > > >
> > > > > | GB non-polar solvation energies calculated with gbsa=2
> > > > >
> > > > > ~
> > > > > and what I've found in the progress.log
> > > > >
> > > > >
> > > > > DecompError: Mismatch in number of decomp terms!
> > > > >
> > > > > Error occured on rank 0.
> > > > >
> > > > > Exiting. All files have been retained.
> > > > >
> > > > > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> > > > >
> > > > >
> > > > > What should I fix here to run it correctly?
> > > > >
> > > > >
> > > > >
> > > > > James
> > > > >
> > > > _______________________________________________
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> > > >
> > >
> > >
> > >
> > > --
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> > imprisoned
> > > here could not dream of heaven?
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>
>
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Received on Tue Feb 03 2015 - 13:00:03 PST
