diff --git a/apps/protein_folding/helixfold3/helixfold/inference.py b/apps/protein_folding/helixfold3/helixfold/inference.py
index 8a862279..57fd692c 100644
--- a/apps/protein_folding/helixfold3/helixfold/inference.py
+++ b/apps/protein_folding/helixfold3/helixfold/inference.py
@@ -453,6 +453,12 @@ def split_prediction(pred, rank):
 def main(cfg: DictConfig):
     logging.set_verbosity(cfg.logging_level)
 
+    if cfg.msa_only == True:
+        logging.warning(f'Model inference will be skipped because MSA-only mode is required.')
+        logging.warning(f'Use CPU only')
+        paddle.device.set_device("cpu")
+        
+
     """main function"""
     new_einsum = os.getenv("FLAGS_new_einsum", True)
     print(f'>>> PaddlePaddle commit: {paddle.version.commit}')
@@ -505,6 +511,8 @@ def main(cfg: DictConfig):
             model.helixfold.set_state_dict(pd_params['model'])
         else:
             model.helixfold.set_state_dict(pd_params)
+
+    
     
     if cfg.precision == "bf16" and cfg.amp_level == "O2":
         raise NotImplementedError("bf16 O2 is not supported yet.")
@@ -531,6 +539,10 @@ def main(cfg: DictConfig):
         with open(features_pkl, 'wb') as f:
             pickle.dump(feature_dict, f, protocol=4)
 
+    if cfg.msa_only == True:
+        logging.warning(f'Model inference is skipped because MSA-only mode is required.')
+        exit()
+
     feature_dict['feat'] = batch_convert(feature_dict['feat'], add_batch=True)
     feature_dict['label'] = batch_convert(feature_dict['label'], add_batch=True)