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relax - P6G molecule

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relax - P6G molecule
#1

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,

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Wed, 2016-11-30 05:01
allan.ferrari

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

 

Wed, 2016-11-30 06:42
sheehajh

Jonathan,

It has worked. Just what I needed. 

Thank you.

Állan.

Thu, 2016-12-01 07:31
allan.ferrari

Assuming that A) your molecule is from a published PDB and B) 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.

Wed, 2016-11-30 09:18
smlewis