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bigginlab / ABFE_workflow

This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.
GNU General Public License v3.0
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Trying to access undeclared variable: input_sdf_ #19

Closed Nithishwer closed 1 year ago

Nithishwer commented 1 year ago

Executing bash example_execution_gmx.sh ends up with:

Traceback (most recent call last): File "/biggin/b211/reub0138/mambaforge/envs/abfe/bin/cli-abfe-gmx", line 12, in sys.exit(main()) File "/biggin/b211/reub0138/Projects/abfe/IrfansPaper/ABFE_workflow-main/abfe_cli/ABFECalculatorGmx.py", line 50, in main res = calculate_abfe_gmx(input_dir=args.gmx_files_root_dir, out_root_folder_path=args.output_dir_path, approach_name=args.project_name, File "/biggin/b211/reub0138/Projects/abfe/IrfansPaper/ABFE_workflow-main/abfe/calculate_abfe_gmx.py", line 70, in calculate_abfe_gmx job_approach_file_path = build_approach_flow(approach_name=approach_name, File "/biggin/b211/reub0138/Projects/abfe/IrfansPaper/ABFE_workflow-main/abfe/orchestration/build_approach_flow.py", line 23, in build_approach_flow generate_conf.generate_approach_conf(out_path=approach_conf_path, TypeError: generate_approach_conf() missing 1 required positional argument: 'small_mol_ff'

build_approach_flow.py fails to provide small_mol_ff as argument to generate_conf.generate_approach_conf()

Not sure how to deal with this.

RiesBen commented 1 year ago

hm... I see, I think I fixed this with: https://github.com/bigginlab/ABFE_workflow/commit/b3df0c5f1774bf416c477574c12a8f23839f8bc6 and https://github.com/bigginlab/ABFE_workflow/commit/0fb9101b405f8669dee4ee676df6f8a9fa69c434

Can you try the script again?

Nithishwer commented 1 year ago

I think this might be taken care of. But I am getting another error raised in #21

Thanks