update

gentop.py

@@ -19,8 +19,13 @@ def generate_gmx_top_files(directory, num_cores, forcefield="amber99sb-ildn", wa
     # Iterate over each PDB file and execute the GROMACS command
     for pdb_file in pdb_files:
         name = pdb_file.stem  # Extract the name without the '.pdb' extension
+        parent = pdb_file.parent
         output_gro = f"{name}.gro"
-        topol_file = "topol.top"
+        topol_file = f"{name}_topol.top"
+
+        # Check if topol_file already exists, and if so, skip this task
+        if Path(topol_file).exists():
+            continue
 
         # Construct the command
         cmd = [
@@ -35,7 +40,7 @@ def generate_gmx_top_files(directory, num_cores, forcefield="amber99sb-ildn", wa
         ]
 
         # Run the command and capture the standard error (stderr) to a log file
-        log_file = pdb_file.absolute().parent.joinpath(f"{name}_gentop.log")
+        log_file = parent.joinpath(f"{name}_topol.log")
         with open(log_file, "w") as log:
             subprocess.run(cmd, check=True, cwd=directory, stderr=log)