# How to introduce point mutations in a protein structure?

I want to introduce point mutations to a protein PDB file and automatically predict the 3D coordinates of a new amino acid residue in the mutated protein.

I used interactive Schrodinger's Maestro tool to mutate residues and minimize them to avoid clashes, however this time i want to automate the task and use some open source tools.

Is there any free software for this task?

VMD would work for sure, I believe PyMOL too. They are both graphical interfaces but you can start them in text only mode (or just import pymol in a python script and use the Python API). They are free for particulars and academics, but given their renown you may already be using them.