Update README.md

- Add proper usage for pdb_mutate.py (former mutate.py). Changed example to match input files format

README.md

@@ -203,23 +203,23 @@ Usage:
     where inputfiles are a list of PDB files to be concatenated
 ```
 
-#### mutate.py
-A python script to mutate residues for HADDOCK. A PDB file and a mutation list file are used as input, and the output is/are corresponding PDB file(s) of mutant(s). The format of mutation in the mutation list file is "ResidueID ResidueName ChainID", The ResidueName is the residue mutated to.
+#### pdb_mutate.py
+A python script to mutate residues for HADDOCK. A mutation list file is used as input, and the output is/are corresponding PDB file(s) of mutant(s). The format of mutation in the mutation list file is "PDBid ChainID ResidueID ResidueNameWT ResidueNameMut".
 
 
 Usage:
 ```bash
-    ./mutate.py <PDBfile> <mutation list file>
+    ./pdb_mutate.py <mutation list file>
 ```
 
 Example:
 ```bash
-./mutate.py 1A22.pdb mut_1A22.list
+./pdb_mutate.py mut_1A22.list
 
 ## In  mut_1A22.list, the residue 14, 18 and 21 in chain A will be mutated to ALA:
-## 14 ALA A
-## 18 ALA A
-## 21 ALA A
+## 1A22.pdb A 14 MET ALA
+## 1A22.pdb A 18 HIS ALA
+## 1A22.pdb A 21 HIS ALA
 ```
 
 #### pdb_strict_format.py