`analyze_results.py`: Could not find a path to connect nodes AAA and BBB. Cannot go on.

[Liaokang123456]

After I finished the "run runall.sh", I got the file "tutorial.tgz"; and I run “analyze_results.py --input tutorial.tgz --units kcal --output_uncompress_directory tutorial --center_molecule=FXR_12” then I got the error like this,

My gromacs version : gmx_mpi 2021.7 alchemlyb_version 0.6.0

[VesperChen01]

I'm having the same problem.

$ analyze_results.py --input tutorial.tgz --units kcal --output_uncompress_directory tutorial --center_molecule=C-7 All available analysis will be run ================== Pairwise ΔΔG ================== Perturbation protein water C-7→d-2 -5.3±0.1 kcal/mol -4.9±0.1 kcal/mol ΔΔG = -0.4±0.1 kcal/mol

=================== STACK INFO =================== File "./analyze_results.py", line 1821, in method=arguments.center_ddg_method) File "./analyze_results.pyanalyze_results.py", line 1039, in ddg_to_center_ddg current_verbosity=verbosity) File "./analyze_results.pyos_util.py", line 307, in local_print formatted_string = '\n{:=^50}\n{}{:=^50}\n'.format(' STACK INFO ', ''.join(traceback.format_stack()), =================== STACK INFO =================== [ERROR] Could not find a path to connect nodes C-15 and C-7. Cannot go on. Check the perturbations and your input graph. Alternatively, rerun with no_checks to force execution and ignore this error. Traceback (most recent call last): File "./analyze_results.pyanalyze_results.py", line 1024, in ddg_to_center_ddg ddg_to_center[each_node] = sum_path(ddg_graph, each_path, ddg_key=ddg_key) File "./analyze_results.pyanalyze_results.py", line 986, in sum_path raise networkx.exception.NetworkXNoPath('Edge between {} {} not found in graph {}'.format(node_i, node_j, g0)) networkx.exception.NetworkXNoPath: Edge between C-7 C-15 not found in graph DiGraph with 6 nodes and 5 edges

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "./analyze_results.pyanalyze_results.py", line 1821, in method=arguments.center_ddg_method) File "./analyze_results.pyanalyze_results.py", line 1040, in ddg_to_center_ddg raise networkx.exception.NetworkXNoPath(error) networkx.exception.NetworkXNoPath: Edge between C-7 C-15 not found in graph DiGraph with 6 nodes and 5 edges

[VesperChen01]

@Liaokang123456 After checking the log file, I found a segmentation fault, which may be caused by a system crash during the gmx_mpi runtime. Therefore, the task was not fully completed in runall.sh. Please check the integrity of the files in each lambda folder in the md file, such as .gro. If any files are missing, you can simply rerun the commands in the runall.sh folder.

"Please let me know if there are any mistakes."

[luancarvalhomartins]

These errors are caused by the lack of data for the perturbations in the error. It means something went wrong with the FEP. Please, check the logs to see why.

I apologize for the output being cryptic. I am rewriting that message to make it more informative.

[luancarvalhomartins]

Please, feel free to fill a new issue in case the FEP problem seems a bug.

Thank you!