# cartfrag_overlap error while running hybridize protocol

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cartfrag_overlap error while running hybridize protocol
#1

Hi,

I am trying to run the hybridize protocol. Every time during the stage 4 of the protocol, I get the following:

protocols.hybridization.HybridizeProtocol: Realigning template domains to stage1 pose.
core.util.switchresiduetypeset: [ WARNING ] When switching to a centroid ResidueTypeSet:  Pose already contains centroid ResidueTypes.
protocols.hybridization.CartesianHybridize: RUNNING FOR 4 MACROCYCLES
protocols.hybridization.CartesianHybridize:  total_res=767   prot_res=767
protocols.hybridization.CartesianHybridize: CYCLE 1
protocols.hybridization.CartesianHybridize:   setting bonded weight = 0
protocols.hybridization.CartesianHybridize:   setting bonded angle weight = 0
protocols.hybridization.CartesianHybridize:   setting bonded length weight = 0
protocols.hybridization.CartesianHybridize:   setting bonded torsion weight = 0
protocols.hybridization.CartesianHybridize:   setting cst    weight = 0.5
protocols.hybridization.CartesianHybridize:   setting vdw    weight = 0.1
core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (767)
core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (767)

ERROR: Assertion cartfrag_overlap_>=1 && cartfrag_overlap_<=len/2 failed.
ERROR:: Exit from: src/protocols/hybridization/CartesianHybridize.cc line: 340

I actually tried to manually set the cartfrag_overlap tag to 0 so that it wouldn't throw this exception. But, I observe it anyway.

What is the purpose of cartfrag_overlap? I couldn't find any document or any pointers. Also, what is triggering this issue in the first place? is there a way to fix this issue?

Thanks

Post Situation:
Thu, 2017-12-21 10:24
sn

Setting cartfrag_overlap to zero isn't going to help you here. (The cartfrag_overlap_>=1 means it needs to be at least 1).

The core issue is your fragments file. The cartfrag_overlap controls how your fragments are being applied.  (Basically, how much overlap on each end your fragments need.) By default this is 2, which means you need your fragments to be at least 4 residues long. But this is your *long* fragments, which typically are the 9-mer fragments.

One thing to check is if you've messed up your fragment file specification, and have accidentally given the 3-mer fragments to the 9-mer fragment option.  (I assume you're not deliberately changing the length of your fragments.) If that's not the issue, I'd recommend regenerating your fragment files, as it's possible that they've gotten corrupted.

Mon, 2018-01-15 16:07
rmoretti

Thank you Rocco.

I experienced the same error.

However, but when I fixed 3mer_frag to 3mer and 9mer_frag to 9mer in rosetta_scripts xml, it is solved.

Mon, 2019-12-30 11:43
dnamkr