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Docking between peptide and lipid-biayer

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Docking between peptide and lipid-biayer

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

You'll need to provide parameters for the lipid molecules you have in the input molecule. See 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, 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