Errors Rosetta symm refine

[Anonymous]

Hi  Rosetta Users,

I just started trying the Rossetta symm refinement by using the default settings. However, I ran into the following error messages,

[ERROR] Exception caught by JobDistributor for job chain_B_symm_0001

[ERROR] EXCN_utility_exit has been thrown from: src/core/conformation/Conformation.cc line: 890

ERROR: Can’t create a polymer bond after residue 4 due to incompatible type: PRO:CtermTruncation

….

As suggested by the tutorial, I used the “make symm .pl” to generate the symm file and gave only one chain (chain_B) as the refinement inputs. 

Does anyone have run into similar problems? Any thought would be appricated. Thanks again!

 

Thanks,

Ming

[Anonymous]

Do you just have 4 residues in the monomer, or is there something funky happening between the 4th & 5th residues in the protein?

I’m not quite sure why, but it looks like it’s thinking that there’s missing density after residue number 4, but *not* thinking that there’s missing density before residue number 5.

One thing you may want to try is to “clean” the PDB, to remove extraneous things in the PDB that may be messing things up. There’s a script that will do it at tools/protein_tools/scripts/clean_pdb.py, but you can also just delete anything that’s not an ATOM line in the PDB.

[Anonymous]

Do you just have 4 residues in the monomer, or is there something funky happening between the 4th & 5th residues in the protein?

I’m not quite sure why, but it looks like it’s thinking that there’s missing density after residue number 4, but *not* thinking that there’s missing density before residue number 5.

One thing you may want to try is to “clean” the PDB, to remove extraneous things in the PDB that may be messing things up. There’s a script that will do it at tools/protein_tools/scripts/clean_pdb.py, but you can also just delete anything that’s not an ATOM line in the PDB.

[Anonymous]

Do you just have 4 residues in the monomer, or is there something funky happening between the 4th & 5th residues in the protein?

I’m not quite sure why, but it looks like it’s thinking that there’s missing density after residue number 4, but *not* thinking that there’s missing density before residue number 5.

One thing you may want to try is to “clean” the PDB, to remove extraneous things in the PDB that may be messing things up. There’s a script that will do it at tools/protein_tools/scripts/clean_pdb.py, but you can also just delete anything that’s not an ATOM line in the PDB.

[Author]

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