# Docking between peptide and lipid-biayer

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Docking between peptide and lipid-biayer
#1

Dear friends
I want make a docking between peptide and lipid-bibayer (rscb: 2msc). I load pdb using pose_from_rscb. But the lipid cann't be identified by pyrosetta. Is there any function for resoleing this problem? Thanks a lot.

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Thu, 2017-10-26 08:35
sprinkle166

You'll need to provide parameters for the lipid molecules you have in the input molecule. See https://www.rosettacommons.org/demos/latest/tutorials/prepare_ligand/prepare_ligand_tutorial for a tutorial on how to do this.

Alternatively, you may just want to use the automatic generation of parameters. If you add the -load_PDB_components option to the intialization of PyRosetta, it can attempt to autogenerate missing ligand parameters from the PDB Chemical Components Dictionary file. This can be downloaded from  http://www.wwpdb.org/data/ccd, and either can be placed into the Rosetta database (in database/chemical/), or can be specified by passing the path to the file with the -PDB_components_file option. -- Keep in mind, though, that the from-CCD generation is rather simplistic. It sufficies for having the ligand be present, but the molfile_to_params way allows you more control of how the ligand is set up and how it's sampled.

A final caveat -- peptide/lipid interactions are a rather unexplored territory for Rosetta. You're exploring new ground. Be aware that things might not work right-off-the-bat, and that you'll need to do a fair amount of testing and benchmarking, and will likely need to adjust/come up with new protocols.

Fri, 2017-12-01 10:34
rmoretti