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luancarvalhomartins / PyAutoFEP

PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods
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Failed to run gmx make_ndx. Error code 11 #99

Open camputchem opened 1 year ago

camputchem commented 1 year ago

I am running the tutorial and getting following error message. I am guessing the files are created on the fly in tmp directory and getting deleted as I can't find those files. Any suggestions?

================== Align poses =================== Molecule FXR_12 aligned ================ Working on pairs ================ Perturbation Pose Coordinates ============ Working on FXR_12-FXR_74 ============ FXR_12→FXR_74 ================ Building system =================

=================== STACK INFO =================== File "/usr/local/PyAutoFEP/prepare_dual_topology.py", line 4241, in build_data = prepare_complex_system(structure_file=arguments.structure, File "/usr/local/PyAutoFEP/os_util.py", line 549, in wrap_trace return f(*args, **kwargs) File "/usr/local/PyAutoFEP/prepare_dual_topology.py", line 703, in prepare_complex_system make_index(build_files_dict['index_ndx'], build_files_dict['fullsystem_pdb'], index_groups, selection_method, File "/usr/local/PyAutoFEP/prepare_dual_topology.py", line 1906, in make_index gmx_data = os_util.run_gmx(gmx_bin, index_cmd, input_data='{}\nq\n'.format(groups_str), File "/usr/local/PyAutoFEP/os_util.py", line 154, in run_gmx local_print('Failed to run {} {}. Error code {}.\nCommand line was: {}\n\nstdout:\n{}\n\nstderr:\n{}' File "/usr/local/PyAutoFEP/os_util.py", line 307, in local_print formatted_string = '\n{:=^50}\n{}{:=^50}\n'.format(' STACK INFO ', ''.join(traceback.format_stack()), =================== STACK INFO =================== [ERROR] Failed to run gmx make_ndx. Error code -11. [ERROR] Command line was: ['gmx', 'make_ndx', '-n', '/tmp/tmpofcvryjn/tutorial/FXR_12-FXR_74/protein/build_system_160710_13072023/index.ndx', '-o', '/tmp/tmpofcvryjn/tutorial/FXR_12-FXR_74/protein/build_system_160710_13072023/index.ndx'] [ERROR] [ERROR] stdout: [ERROR] [ERROR] [ERROR] stderr: [ERROR] :-) GROMACS - gmx make_ndx, 2023 (-: [ERROR] [ERROR] Executable: /usr/local/gromacs/bin/gmx [ERROR] Data prefix: /usr/local/gromacs [ERROR] Working dir: /home/rajan/Desktop/fep_tut [ERROR] Command line: [ERROR] gmx make_ndx -n /tmp/tmpofcvryjn/tutorial/FXR_12-FXR_74/protein/build_system_160710_13072023/index.ndx -o /tmp/tmpofcvryjn/tutorial/FXR_12-FXR_74/protein/build_system_160710_13072023/index.ndx [ERROR] [ERROR]

xy21hb commented 1 year ago

image

Change the Gromacs version to the designated.

luancarvalhomartins commented 1 year ago

Yes, GROMACS 2023 won't work, but the error should not come in the make_ndx. I suggest running with output_hidden_temp_dir=False so we can have the intermediate files to check.

Also note that this maybe a version of #6. In case, it should be fixed by using output_hidden_temp_dir=False.