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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Received on Tue Feb 03 2015 - 07:30:02 PST
