text: user7057: I have multiple ligands (in pdb format) which I want to try and dock to various proteins.
  But for each ligand I have only a single conformation (by which I meant the spatial relationship between it's atoms, not its position relative to the target protein).
  How do I generate other possible conformations?
  Is there a generally used tool for that? 
  
  user7057: One option I found was Frog2
  https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::Frog2
  https://github.com/tuffery/Frog2
  From an input of a mol2 or sdf file it creates a plethora of conformers, which can be outputted as a pdb file
  
  user6322: Open babel
  The most commonly used tool is open-babel (obabel). It seems annoying that you have to specify the number of conformers, but this is because if you get something like retinol, the number of conformers is huge. The command from the documentation is:
  obabel startingConformer.mol -O ga_conformers.sdf --conformer --nconf 30
     --score rmsd --writeconformers
  
  An alternative argument is --confab which will pick each representative of a RMSD cutoff cluster.
  Do note that 2D representations and un-protonated molecules will need extra command line arguments.
  RDKit
  You can also generate conformers in RDkit, but I think this is beyond your requirements, but I thought it may be good to mention the essential compchem python library.
  
original_text: 7057: <p>I have multiple ligands (in pdb format) which I want to try and dock to various proteins.</p>
  
  <p>But for each ligand I have only a single conformation (by which I meant the spatial relationship between it's atoms, not its position relative to the target protein).</p>
  
  <p>How do I generate other possible conformations?
  Is there a generally used tool for that? </p>
   7057: <p>One option I found was Frog2</p>
  
  <p><a href="https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::Frog2" rel="nofollow noreferrer">https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::Frog2</a></p>
  
  <p><a href="https://github.com/tuffery/Frog2" rel="nofollow noreferrer">https://github.com/tuffery/Frog2</a></p>
  
  <p>From an input of a <code>mol2</code> or <code>sdf</code> file it creates a plethora of conformers, which can be outputted as a <code>pdb</code> file</p>
   6322: <h2>Open babel</h2>
  
  <p>The most commonly used tool is <code>open-babel</code> (obabel). It seems annoying that you have to specify the number of conformers, but this is because if you get something like retinol, the number of conformers is huge. The command from the <a href="https://open-babel.readthedocs.io/en/latest/3DStructureGen/multipleconformers.html" rel="nofollow noreferrer">documentation</a> is:</p>
  
  <pre><code>obabel startingConformer.mol -O ga_conformers.sdf --conformer --nconf 30
     --score rmsd --writeconformers
  </code></pre>
  
  <p>An alternative argument is <code>--confab</code> which will pick each representative of a RMSD cutoff cluster.</p>
  
  <p>Do note that 2D representations and un-protonated molecules will need extra command line arguments.</p>
  
  <h2>RDKit</h2>
  
  <p>You can also generate conformers in RDkit, but I think this is beyond your requirements, but I thought it may be good to mention the essential compchem python library.</p>
  