cannot open gmx_MMPBSA_ana

[SITI AISHAH SUFIRA BINTI NOR HISHAMUDDIN]

Hi! I already installed gmxMMPBSA and already run the MMPBSA using the finalized output from CHARMM-Gui. I ran this program using mpirun 

$ mpirun -np 20 gmx_MMPBSA -O -i mmpbsa.in -cs md.tpr -ci index_protein.ndx -cg 16 17 -ct md_center.xtc -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -cp topol.top

the process was going smoothly until i want to see the result using gma_MMPBSA_ana.

this is the error output.

multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
  File "/home/psr2021/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 3803, in get_loc
    return self._engine.get_loc(casted_key)
  File "pandas/_libs/index.pyx", line 138, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/index.pyx", line 165, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/hashtable_class_helper.pxi", line 5745, in pandas._libs.hashtable.PyObjectHashTable.get_item
  File "pandas/_libs/hashtable_class_helper.pxi", line 5753, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'delta'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/psr2021/anaconda3/envs/gmxMMPBSA/lib/python3.9/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "/home/psr2021/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/analyzer/dialogs.py", line 585, in run_process
    obj = obj_method(**v['args']) if v['args'] else obj_method()
  File "/home/psr2021/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/API.py", line 829, in get_ana_data
    dict(data=decomp[level][level1][level2][level3], level=item_lvl,
  File "/home/psr2021/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/pandas/core/frame.py", line 3804, in __getitem__
    return self._getitem_multilevel(key)
  File "/home/psr2021/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/pandas/core/frame.py", line 3855, in _getitem_multilevel
    loc = self.columns.get_loc(key)
  File "/home/psr2021/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/pandas/core/indexes/multi.py", line 2916, in get_loc
    loc = self._get_level_indexer(key, level=0)
  File "/home/psr2021/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/pandas/core/indexes/multi.py", line 3263, in _get_level_indexer
    idx = self._get_loc_single_level_index(level_index, key)
  File "/home/psr2021/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/pandas/core/indexes/multi.py", line 2849, in _get_loc_single_level_index
    return level_index.get_loc(key)
  File "/home/psr2021/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 3805, in get_loc
    raise KeyError(key) from err
KeyError: 'delta'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/psr2021/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/analyzer/dialogs.py", line 598, in run
    for result in imap_unordered_it:
  File "/home/psr2021/anaconda3/envs/gmxMMPBSA/lib/python3.9/multiprocessing/pool.py", line 870, in next
    raise value
KeyError: 'delta'
Aborted (core dumped)

Can you please clarify this problem? Thank you so mcuh!

[Mario Sergio Valdes]

Can you tell us which version you are using? You can check all the specifications in the head of the gmx_MMPBSA.log file.

[Mario Sergio Valdes]

Please attach the file gmx_MMPBSA.log here

[Mario Sergio Valdes]

Are you running in the WSL?

The WSL requires the installation of an x-server to run GUIs. Check this tutorial (https://learn.microsoft.com/en-us/windows/wsl/tutorials/gui-apps)

[Muhamad Alif Bin Che Nordin]

hi mario

i happen to come across this error today.

Fyi, im using gmx_MMPBSA v1.6.3.

i created a bash file to process my trajectory and structure files before submitting to gmx_MMPBSA for calculation.
Attached is the terminal window in text file and log file.

help me please. thanks

--
You received this message because you are subscribed to the Google Groups "gmx_MMPBSA" group.
To unsubscribe from this group and stop receiving emails from it, send an email to gmx_mmpbsa+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/gmx_mmpbsa/5c1cd62b-367f-42ef-81f9-f667011e5a4fn%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

--

ALIF NORDIN.

Assistant Registrar N41
PJK, UniSHAMS

04-4155095

0174070407

01140737157

Bachelor of Biomedicine (Hons.), Master of Science (Biomedicine)

Cancer Immunology · Medical Virology · Molecular Dynamics Simulation

Ordinary Member of Malaysian Society for Biochemistry and Molecular Biology (MSBSB) [Membership No. OM-2019-044]

Pusat Jaminan Kualiti
Universiti Islam Antarabangsa Sultan Abdul Halim Mu'adzam Shah  (UniSHAMS)

[mariosergi...@gmail.com]

Can you show the conda list terminal output? This problem can be related to the pandas package version

[Muhamad Alif Bin Che Nordin]

sure. conda list is as attached. thanks

To view this discussion on the web visit https://groups.google.com/d/msgid/gmx_mmpbsa/d17b530a-59f0-47a4-b1aa-be6fe1e3baaan%40googlegroups.com.

For more options, visit https://groups.google.com/d/optout.