Re: [AMBER] Error with MMPBSA - per residue decomposition

From: Prasanth G, Research Scholar <prasanthghanta.sssihl.edu.in> Date: Thu, 18 Jun 2020 22:48:51 +0530

----
I was able to get the FINAL_RESULTS_MMPBSA.dat but was not able to get the
FINAL_DECOMP_MMPBSA.dat file. the error is as follows:
  File "/usr/local/amber16/bin/MMPBSA.py.MPI", line 109, in <module>
    app.write_final_outputs()
  File
"/usr/local/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line
645, in write_final_outputs
    self.normal_system, self.mutant_system, self.mut_str, self.pre)
  File
"/usr/local/amber16/lib/python2.7/site-packages/MMPBSA_mods/output_file.py",
line 762, in write_decomp_binding_output
    pb_bind.parse_all()
  File
"/usr/local/amber16/lib/python2.7/site-packages/MMPBSA_mods/amber_outputs.py",
line 2112, in _parse_all_csv
    self._parse_all_begin()
  File
"/usr/local/amber16/lib/python2.7/site-packages/MMPBSA_mods/amber_outputs.py",
line 1956, in _parse_all_begin
    raise DecompError('Mismatch in number of decomp terms!')
DecompError: Mismatch in number of decomp terms!
Error occured on rank 0.
Exiting. All files have been retained
-----
Can you please help me fix this issue.
Thank you.
On Sat, Jun 13, 2020 at 1:21 PM Prasanth G, Research Scholar <
prasanthghanta.sssihl.edu.in> wrote:
> 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.
>
-- 
Regards,
Prasanth.
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