On Tue, Sep 26, 2017 at 3:13 AM, Sergey Samsonov
<sergey.samsonov.ug.edu.pl> wrote:
> "/users/work/czarek/amber16/lib/python2.7/site-packages/MMPBSA_mods/amber_outputs.py",
> line 1536, in _get_next_term
> internal = float(line[11:20])
> ValueError: could not convert string to float: *********
I'm not certain, but it seems like maybe an energy value overflowed,
producing the asterisks. You can check the frames to see if you have
bad overlaps with the 'check' command from cpptraj (use the GitHub
version of cpptraj since it has a faster 'check' version).
-Dan
> Exiting. All files have been retained.
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> -------------------
>
> If I do decomposition on frames one by one separately, it works for some
> frames without problems but not for others (for the problematic single
> frames I get the same empty output as shown above). Trajectory
> (visually) looks fine, there is no sign of corrupted frames, RMSD and
> other parameters obtained by cpptraj do not seem to be problematic. I
> tried also to rewrite the trajectory into the the old format but the out
> come was identical.
>
> My input:
> -------------------------------
> Input file for GB/decomposition calculation
> &general
> startframe=1, endframe=1000, interval=1,
> verbose=2, keep_files=0,
> /
> &gb
> igb=2,
> /
> &decomp
> idecomp=2
> /
> -------------------------------
> I run MMPBSA in a standard way with all four topogies:
> MMPBSA.py.MPI -O -i decomp.input -o gb_binding.out -cp complex.top -rp
> receptor.top -lp ligand.top -sp ../top.top -y ../mdcrd/md.mdcrd
>
> Thank you very much and cheers,
>
> Sergey
>
> --
> Sergey Samsonov, PhD
> Project Leader at Laboratory of Molecular Modeling,
> Department of Theoretical Chemistry,
> Faculty of Chemistry,
> University of Gdansk
> ul. Wita Stwosza 63
> 80-308 Gdansk, Poland
> phone: +48 58 523 5166
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Wed Sep 27 2017 - 10:30:02 PDT
