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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Received on Tue Feb 03 2015 - 08:00:03 PST
