update error handle

gentop.py

@@ -41,8 +41,11 @@ 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 = parent.joinpath(f"{name}_topol.log")
-        with open(log_file, "w") as log:
-            subprocess.run(cmd, check=True, cwd=directory, stderr=log)
+        try:
+            with open(log_file, "w") as log:
+                subprocess.run(cmd, check=True, cwd=directory, stderr=log)
+        except subprocess.CalledProcessError as e:
+            print(f"Error processing {pdb_file.name}: {e}")
 
 # Example usage
 directory = "pdb_top"  # Replace with your actual directory path