Update README.md

Author: chrischen1

README.md

@@ -13,10 +13,11 @@ optional arguments:
   --input INPUT               Path to input pdb file.
   --output OUTPUT             Path to output folder.
   --method METHOD             Prediction method, can be "EGNN_Full", "se3_Full", "EGNN_esto9" or "EGNN_covariance". Ensemble can be done listing multiple models separated by comma.
-  --cpu                       Force to use CPU.
   --alphafold_prediction      Path to alphafold prediction results.               
   --alphafold_feature_cache   Optional. Can cache AlphaFold features for models of the same sequence.
-  --af2_pdb AF2_PDB           Optional. PDBs from AlphaFold2 predcition for index correction with input pdb
+  --af2_pdb AF2_PDB           Optional. PDBs from AlphaFold predcition for index correction with input pdb when input PDB only contains partial sequence of the AlphaFold results.
+  --cpu                       Optional. Force to use CPU.
+
 ```
 
 ## Requirements: