From a937bd0334ef3c2485345254c1c11a7db0cd6248 Mon Sep 17 00:00:00 2001
From: hotwa <pylyzeng@gmail.com>
Date: Wed, 10 Jan 2024 09:47:01 +0800
Subject: [PATCH] update error handle

---
 gentop.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/gentop.py b/gentop.py
index bfa4df4..4a646d2 100644
--- a/gentop.py
+++ b/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