Seems like your coordinates may have some issues. Try running the
trajectory through the cpptraj 'check' command to see if you have bad
overlaps. Also, you may want to try running a few frames in serial to
see if you have similar problems.
-Dan
On Tue, Aug 25, 2015 at 5:29 AM, <anilkumarsahoo.physics.iisc.ernet.in> wrote:
> Dear AMBER users,
>
> I have installed MMPBSA.py.MPI module of AmberTools14 and am able to
> perform binding energy calculation using that. But when I am including any
> Lipid residue in the system, it is giving the following error
>
> File "/home/anilkumarsahoo/amber14/bin/MMPBSA.py.MPI", line 104, in ?
> app.parse_output_files()
> File "/home/anilkumarsahoo/amber14/bin/MMPBSA_mods/main.py", line 928,
> in parse_output_files
> self.using_chamber)}
> File "/home/anilkumarsahoo/amber14/bin/MMPBSA_mods/amber_outputs.py",
> line 634, in __init__
> AmberOutput._read(self)
> File "/home/anilkumarsahoo/amber14/bin/MMPBSA_mods/amber_outputs.py",
> line 343, in _read
> self._get_energies(output_file)
> File "/home/anilkumarsahoo/amber14/bin/MMPBSA_mods/amber_outputs.py",
> line 661, in _get_energies
> self.data['VDWAALS'].append(float(words[2]))
> ValueError: invalid literal for float(): *************
> Error occured on rank 0.
> Exiting. All files have been retained.
>
>
> My input file for the calculation is given bellow.
>
> &general
> startframe=1, endframe=200, interval=1, keep_files=2, verbose=2,
> netcdf=1, use_sander=1,
> /
> &gb
> igb=2, saltcon=0.0,
> /
>
> Thanks for any help,
> Anil Kumar Sahoo
>
>
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>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Aug 25 2015 - 06:30:05 PDT
