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?
PDBFixer and pyMutate are simple, lightweight, free and open-source. Both don't do any optimizing, though, so you may have to run some molecular dynamics afterward to get what would be the right "orientation".
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.
If you're looking for something a tad more complete and that may adapt the side-chain to the surrounding environment I'd go with Modeller, which provides two example scripts to do point mutations (here and there).
If you don't want to just get the side-chain of this amino-acid right but actually strive to see some general backbone adaptation too then use PyRosetta. It can probably do what all the others do, too, but given it is 1 GB big it may be overkill. Any of the package coupled with molecular dynamics would also do the trick.
