Saw a script provided by Modeller that can quickly mutate a point to any other residues.
Here is the linke <Mutate model python script by Modeller>
To use the script, just type command like the following line:
Example: python mutate_model.py 1t29 1699 LEU A > 1t29.log
Where mutate_model.py is the script provided by Modeller
1t29 is the PDB file name
1699 is the position for mutation
LEU is the new residue
A stands for chain number.
I have test this script at Modeller 9v11, it works very well and quickly.