[AMBER] Error with MMPBSA - per residue decomposition

From: Prasanth G, Research Scholar <prasanthghanta.sssihl.edu.in>
Date: Sat, 13 Jun 2020 13:21:15 +0530

Dear all,
I am interested in carrying out MMPBSA and determine the per residue energy
contribution towards the binding free energy.

My mmpbsa.in looks like this -
------------
Input file for running PB and GB
&general
   endframe=50, verbose=2,interval=5,
   keep_files=1,
   full_traj=1,
   netcdf=1,
   entropy=0,
/
&gb
  igb=5,
/
&pb
  inp=1,
  radiopt=0,
/
&decomp
  idecomp=2, dec_verbose=3,
  print_res=“173, 177, 359, 363, 364, 368, 402, 403, 406, 410, 546, 603,
670”
/
-------------
However on executing the command -
mpirun -np 10 $AMBERHOME/bin/MMPBSA.py.MPI -O -i mmpbsa.in -o
FINAL_RESULTS_MMPBSA.dat -sp ../comsol.prmtop -cp ../comdry.prmtop -rp
../prodry.prmtop -lp ../ligdry.prmtop -y production_mmpbsa_20_30.nc >
progress.log &

I get this error -
---------------
libibverbs: Warning: couldn't open config directory
'/usr/local/etc/libibverbs.d'.
File "/usr/local/amber16/bin/MMPBSA.py.MPI", line 99, in <module>
    app.file_setup()
  File
"/usr/local/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line
141, in file_setup
    create_inputs(INPUT, self.normal_system, self.pre)
  File
"/usr/local/amber16/lib/python2.7/site-packages/MMPBSA_mods/createinput.py",
line 56, in create_inputs
    com_card, rc_card, lc_card =
prmtop_system.Group(INPUT['print_res'],True)
  File
"/usr/local/amber16/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py",
line 541, in Group
    rec_group_type, lig_group_type)
  File
"/usr/local/amber16/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py",
line 591, in _binding_group
    self._select_residues(selection)
  File
"/usr/local/amber16/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py",
line 845, in _select_residues
    raise SelectionError('Invalid selection! Integers expected.')
SelectionError: Invalid selection! Integers expected.
Error occured on rank 0.
Exiting. All files have been retained.
--------------
Request you to help me overcome this issue.
Thank you.

-- 
Regards,
Prasanth.
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Received on Sat Jun 13 2020 - 01:00:03 PDT
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