text: user7150: 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?
  
  user12054: 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.
  
original_text: 7150: <p>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.</p>
  <p>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.</p>
  <p>Is there any free software for this task?</p>
   12054: <p><strong><a href="https://github.com/openmm/pdbfixer" rel="nofollow noreferrer">PDBFixer</a></strong> and <strong><a href="http://mmb.irbbarcelona.org/gitlab/BioExcel/pyMutate" rel="nofollow noreferrer">pyMutate</a></strong> 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 &quot;orientation&quot;.</p>
  <p><strong><a href="https://www.ks.uiuc.edu/Research/vmd/" rel="nofollow noreferrer">VMD</a></strong> would work for sure, I believe <strong><a href="https://pymol.org/2/" rel="nofollow noreferrer">PyMOL</a></strong> too. They are both graphical interfaces but you can start them in text only mode (or just <code>import pymol</code> 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.</p>
  <p>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 <strong><a href="https://salilab.org/modeller/" rel="nofollow noreferrer">Modeller</a></strong>, which provides two example scripts to do point mutations (<a href="https://salilab.org/modeller/8v0/manual/node125.html" rel="nofollow noreferrer">here</a> and <a href="https://salilab.org/modeller/wiki/Mutate%20model" rel="nofollow noreferrer">there</a>).</p>
  <p>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 <strong><a href="http://www.pyrosetta.org/" rel="nofollow noreferrer">PyRosetta</a></strong>. 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.</p>
  