I'm trying to make a homology model for a Zn-binding metalloenzyme based on some other members of the same family that have been crystallized. My general strategy has been to do comparative modeling first with limited redesign of the loops to get the main structural features in place, and then use the loopmodel appliation to refine the structure a bit more. I had trouble incorporating the Zn residue into the comparative modeling application, so I inserted the Zn into the PDB result and now I'm trying to include it in the loop modeling step.
So far, I can get something fairly representative by manually including constraint files to define the Zn placement; however, I want to use the auto_setup_metals flag if I can as I imagine it might be more effective. In the fullatom state, the flag appears to recognize the correct binding residues (the connections are correct in the sequence), but the application crashes shortly after because I believe it is trying to include the newly named residue types in the centroid stage. I have been probing the options and code a bit and I haven't been able to find why it's switching to centroid in this order. Kind of hard to describe I think, so I attached the output of the loopmodel debug application. The relevant section is here:
protocols.loop_build.LoopBuildMover: Annotated sequence of pose: M[MET:NtermProteinFull]ALLTAETFRLQFNNKRRLRRPYYPRKALLCYQLTPQNGSTPTRGYFENKKKCH[HISND1_connect]AEICFINEIKSMGLDETQCYQVTCYLTWSPC[CYSSG_connect]SSC[CYSSG_connect]AWELVDFIKAHDH[HIS_D]LNLGIFASRLYYH[HIS_D]WCKPQQKGLRLLCGSQVPVEVMGFPKFADCWENFVDHEKPLSFNPYKMLEELDKNSRAIKRRLERIKS[SER:CtermProteinFull]Z[ZNZN_connectZN_connect2ZN_connect3]
protocols.looprelax: ==== Loop protocol: =================================================
protocols.looprelax: remodel no
protocols.looprelax: intermedrelax no
protocols.looprelax: refine refine_kic_with_fragments
protocols.looprelax: relax no
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
core.chemical.ResidueTypeSet: Finished initializing centroid residue type set. Created 1042 residue types
can not find a residue type that matches the residue HISND1_connectat position 54
ERROR: core::util::switch_to_residue_type_set fails
ERROR:: Exit from: src/core/util/SwitchResidueTypeSet.cc line: 323
Anyone happen to know why it's trying to initialize the centroid residue type set, and why it thinks the HISND1_connect is in the sequence even though that should be the fullatom sequence (I think)? Any advice would be appreciated!
I attached a debug run log, the input PDB file, and flags file to this post. Thanks!
*edited to change the reference to the flag from auto_setup_ligands to the correct auto_setup_metals