relax – P6G molecule – Rosetta Commons

This topic has 9 replies, 3 voices, and was last updated 7 years, 10 months ago by Anonymous.

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- November 30, 2016 at 1:01 pm #2556
  Anonymous
  I would like to relax some decoys with a small molecule, P6G, in a specific location, extracted from a homologous protein from PDB. For doing so, I have saved a PDB file with the protein as chain A and P6G as chain B. Rosetta does not recognize P6G as a residue, for obvious reasons.
  
  Is there a straightforward way to run the relax protocol in this situation?
  
  Best,
- November 30, 2016 at 2:42 pm #11990
  Anonymous
  Hi Allan,
  
  Have you already worked through the tutorial here?
  
  https://www.rosettacommons.org/demos/latest/tutorials/prepare_ligand/prepare_ligand_tutorial
  
  Adapting that procedure is probably the best way to handle your P6G ligand.
  
  Hope that helps!
  
  -Jonathan
- November 30, 2016 at 2:42 pm #12511
  Anonymous
  Hi Allan,
  
  Have you already worked through the tutorial here?
  
  https://www.rosettacommons.org/demos/latest/tutorials/prepare_ligand/prepare_ligand_tutorial
  
  Adapting that procedure is probably the best way to handle your P6G ligand.
  
  Hope that helps!
  
  -Jonathan
- November 30, 2016 at 2:42 pm #13032
  Anonymous
  Hi Allan,
  
  Have you already worked through the tutorial here?
  
  https://www.rosettacommons.org/demos/latest/tutorials/prepare_ligand/prepare_ligand_tutorial
  
  Adapting that procedure is probably the best way to handle your P6G ligand.
  
  Hope that helps!
  
  -Jonathan
- November 30, 2016 at 5:18 pm #11993
  Anonymous
  Assuming that A) your molecule is from a published PDB and you don’t need the molecule itself to move internally, try https://www.rosettacommons.org/docs/wiki/build_documentation/Build-Documentation#setting-up-rosetta-3_obtaining-additional-files_pdb-chemical-components-dictionary
  
  This loads the PDB-published dictionary of chemical entities as residues Rosetta can recognize.
- November 30, 2016 at 5:18 pm #12514
  Anonymous
  Assuming that A) your molecule is from a published PDB and you don’t need the molecule itself to move internally, try https://www.rosettacommons.org/docs/wiki/build_documentation/Build-Documentation#setting-up-rosetta-3_obtaining-additional-files_pdb-chemical-components-dictionary
  
  This loads the PDB-published dictionary of chemical entities as residues Rosetta can recognize.
- November 30, 2016 at 5:18 pm #13035
  Anonymous
  Assuming that A) your molecule is from a published PDB and you don’t need the molecule itself to move internally, try https://www.rosettacommons.org/docs/wiki/build_documentation/Build-Documentation#setting-up-rosetta-3_obtaining-additional-files_pdb-chemical-components-dictionary
  
  This loads the PDB-published dictionary of chemical entities as residues Rosetta can recognize.
- December 1, 2016 at 3:31 pm #11997
  Anonymous
  Jonathan,
  
  It has worked. Just what I needed.
  
  Thank you.
  
  Állan.
- December 1, 2016 at 3:31 pm #12518
  Anonymous
  Jonathan,
  
  It has worked. Just what I needed.
  
  Thank you.
  
  Állan.
- December 1, 2016 at 3:31 pm #13039
  Anonymous
  Jonathan,
  
  It has worked. Just what I needed.
  
  Thank you.
  
  Állan.
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