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GeneralizedKIC disulfide closure

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GeneralizedKIC disulfide closure
#1

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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Tue, 2022-08-16 13:32
Ken

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

Tue, 2022-08-16 23:01
vmulligan

Thanks Vikram!  I can't believe it was a typo.

Best,

Ken

Wed, 2022-08-17 08:04
Ken