Merge pull request #23 from Nithishwer/bug_fix

fixed submit boolean and json import
bigginlab · May 3, 2024 · e58b463 · e58b463
2 parents 561deeb + 776f1c6
commit e58b463
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Showing 2 changed files with 5 additions and 3 deletions.
diff --git a/src/abfe/scripts/preparation/parametrize.py b/src/abfe/scripts/preparation/parametrize.py
@@ -49,7 +49,9 @@ def parameterize(input_molecule, output_dir, hmr=False, input_molecule_name="MOL
         interchange.to_gro(os.path.join(dir_name, "out.gro"))
         interchange.to_top(os.path.join(dir_name, "out.top"))
         interchange.to_prmtop(pmd_top_file)
-
+
+	# Define the path to the gro file
+        gro_coord_file = os.path.join(dir_name, "out.gro")
     elif(ff=="gaff"):
         # input
         system = BSS.IO.readMolecules(input_molecule)

diff --git a/src/abfe_cli/ABFECalculator.py b/src/abfe_cli/ABFECalculator.py
@@ -2,7 +2,7 @@
 
 import glob
 import argparse
-
+import json
 from abfe import calculate_abfe
 from abfe.template import default_slurm_config_path
 
@@ -56,7 +56,7 @@ def main():
                          n_cores_per_job=args.number_of_cpus_per_ligand_job, num_jobs_per_ligand=args.number_of_parallel_ligand_jobs,
                          num_jobs_receptor_workflow=args.number_of_parallel_receptor_jobs,
                          num_replicas=args.number_of_replicates,
-                         submit=args.nosubmit, use_gpu=not bool(args.nogpu), hybrid_job=not bool(args.nohybrid), small_mol_ff=args.small_mol_ff,
+                         submit=not bool(args.nosubmit), use_gpu=not bool(args.nogpu), hybrid_job=not bool(args.nohybrid), small_mol_ff=args.small_mol_ff,
                          cluster_config=cluster_config)
 
     return res