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relax - P6G molecule

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relax - P6G molecule

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?



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Wed, 2016-11-30 05:01

Hi Allan,

Have you already worked through the tutorial here?

Adapting that procedure is probably the best way to handle your P6G ligand.

Hope that helps!



Wed, 2016-11-30 06:42


It has worked. Just what I needed. 

Thank you.


Thu, 2016-12-01 07:31

Assuming that A) your molecule is from a published PDB and B) you don't need the molecule itself to move internally, try

This loads the PDB-published dictionary of chemical entities as residues Rosetta can recognize.

Wed, 2016-11-30 09:18