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
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Ask yourselves, all of you, what power would hell have if those
> imprisoned
> > here could not dream of heaven?
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> >
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Received on Tue Feb 03 2015 - 11:30:03 PST
