[AMBER] Problem In Performing MMPBSA Calculation for System Containing Lipids

From: <anilkumarsahoo.physics.iisc.ernet.in>
Date: Tue, 25 Aug 2015 16:59:38 +0530

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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Received on Tue Aug 25 2015 - 05:30:03 PDT
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