Dear all,
I was able to fix the issue by including the ligand residue number in the
print_res section.
Thank you.
On Thu, Jun 18, 2020 at 10:48 PM Prasanth G, Research Scholar <
prasanthghanta.sssihl.edu.in> wrote:
> Dear all,
> I was able to figure out the mistake,
>
> I modified my script to 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,
> /
> &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",
> /
> ----
> 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.
>
--
Regards,
Prasanth.
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Received on Fri Jun 19 2020 - 13:00:04 PDT
