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
