Hi all,
I have been banging my head against the wall on this for a while now, and I think it's time to get help. Here is my problem. I'm trying to understand how to close loops in a toy example via different residues (head to tail, side-chain/side-chain, disulfide, etc) with GenKIC and I cannot for the life of me understand what the error message is trying to tell me.
Here is what I have done. I have a 7mer peptide and I am able to use GenKIC to close via head-to-tail, but when I try to close the loop via disulfide linkage, it errors out with the message "Mover make_disulfide not found in map".
Here is what I have run that works:
rosetta_scripts.static.linuxgccrelease -nstruct 10 -in:file:s input/CAAWAAC.pdb -in:file:fullatom -write_all_connect_info -parser:protocol xml/closeH2T.xml -jd2:failed_job_exception false -mute protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter core.chemical.AtomICoor core.conformation.Residue
This is the one that errors out:
rosetta_scripts.static.linuxgccrelease -nstruct 10 -in:file:s input/CAAWAAC.pdb -in:file:fullatom -write_all_connect_info -parser:protocol xml/closeDS.xml -jd2:failed_job_exception false -mute protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter core.chemical.AtomICoor core.conformation.Residue
Does anybody know what the error message is complaining about?
Best,
Ken
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Hi, Ken. It looks like the second script has a typo in it. You have named your DeclareBond mover "make_disulfde" (missing an 'i'), but later on in the protocols section you refer to "make_disulfide" (with an 'i').
--Vikram
Thanks Vikram! I can't believe it was a typo.
Best,
Ken