Problems with Ligand Docking
Hi everyone,
I am attempting to run a blind dock of a ligand (chain X) into a protein complex (chains ABCDEF). However, try as I might, I seem to always encounter problems. Currently, despite the fact that the flags I'm using should perturb the ligand by a significant amount, the resulting structures are virtually identical (for all chains) to the starting structure, except all chains have been rotated.
Here are my current command line flags:
-in:path:database /ifs/scratch/saxen/rosetta_database
-in:file:s struct_rpk_C2E.pdb
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