add log

gentop.py

@@ -13,11 +13,6 @@ def generate_gmx_top_files(directory, num_cores, forcefield="amber99sb-ildn", wa
     forcefield (str): Forcefield parameter for GROMACS. Default is "amber99sb-ildn".
     water_model (str): Water model parameter for GROMACS. Default is "tip3p".
     """
-    # Ensure the GMXRC path is sourced if set
-    gmxrc_path = os.getenv("GMXRC_PATH")
-    if gmxrc_path:
-        subprocess.run(f"source {gmxrc_path}", shell=True, executable='/bin/bash')
-
     # Find all PDB files in the specified directory
     pdb_files = Path(directory).glob("*.pdb")
 
@@ -27,18 +22,22 @@ def generate_gmx_top_files(directory, num_cores, forcefield="amber99sb-ildn", wa
         output_gro = f"{name}.gro"
         topol_file = "topol.top"
 
-        # Construct and run the command with the working directory set to 'directory'
+        # Construct the command
         cmd = [
             "mpirun", "-np", str(num_cores),
             "gmx_mpi", "pdb2gmx", 
-            "-f", str(pdb_file), 
+            "-f", pdb_file.absolute().as_posix(), 
             "-o", output_gro, 
             "-ff", forcefield, 
             "-water", water_model, 
             "-ignh", 
             "-p", topol_file
         ]
-        subprocess.run(cmd, check=True, cwd=directory)
+
+        # Run the command and capture the standard error (stderr) to a log file
+        log_file = pdb_file.absolute().parent.joinpath(f"{name}_gentop.log")
+        with open(log_file, "w") as log:
+            subprocess.run(cmd, check=True, cwd=directory, stderr=log)
 
 # Example usage
 directory = "pdb_top"  # Replace with your actual directory path