hi all
I try to dock one metalloprotein (ZN and Ca) to a small protein inhibitor.
I started, as suggested in the session “Working With Metalloproteins in Rosetta”, relaxing the crystal structure of the metalloprotein applying the flag -in:auto_setup_metals, in the full atom mode.
The relaxed structure and protein inhibitor were added to the same pdb file (at 20A of distance )and used as starting coordinates to the docking protocol.
The problem was in the Centroid Docking Phase, I guess.
During the configuration of centroids by auto_setup_metals a Glu-OE1 interaction was not recognized, showing the message below:
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core.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 62 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.04 seconds.
core.util.switchresiduetypeset: SQVRGDLECDEKDAKEWTDTGVRYINEHKLHGYKYALNVIKNIVVVPWDGDWVAVFLKLNLLETECHVLDPTPVKNCTVRPQHNHAVEMDCDVKIMFNVDTFKEDVFAKCHSTPDSVENVRRNCPKCPILLPSQKYNPFRYVELFIVVDQGMVTKNNGDLDKIKARMYELANIVNEILRYLYMHAALVGLEIWSNGDKITVKPDVDYTLNSFAEWRKTDLLTRKKHDNAQLLTAIDFNGPTIGYAYIGSMCHPKRSVAIVEDYSPINLVVAVIMAHEMGHNLGIHHDTDFCSCGDYPCIMGPTISNEPSKFFSNCSYIQCWDFIMKENPQCILNEPLGTDIVSPPVCGNELLEVGEECDCGTPENCQNECCDAATCKLKSGSQCGHGDCCEQCKFSKSGTECRASMSECDPAEHCTGQSSECPADVFHKNGQPCLDNYGYCYNGNCPIMYHQCYALFGADVYEAEDSCFKDNQKGNYYGYCRKENGKKIPCAPEDVKCGRLYCKDNSPGQNNPCKMFYSNDDEHKGMVLPGTKCADGKVCSNGHCVDVAZZZZ
core.util.switchresiduetypeset: can not find a residue type that matches the residue GLU:MP-OE1-connect:MP-OE1-pruneH at position 143
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As stated in the documentation setup interactions in centroid mode for side chains is tricky
Can you give me some advice on this setup?
Thanks
.
