Table 2.
Troubleshooting table
| STEP | PROBLEM | POSSIBLE REASON | SOLUTION |
|---|---|---|---|
| EQUIPMENT | Rosetta does not compile. | Likely to be related to the specific computer operating system and configuration | Seek help on the Rosetta forums, www.rosettacommons.org/forum |
| 4 | Rosetta Antibody encounters error “ sh: blastp: command not found” | The blastp executable is not installed or not in in your $PATH | On the command line, try ‘ which blastp‘ to check if your system has it installed. If needed, download and install BLAST or/and add blastp to your PATH ( export PATH=$PATH:/path/to/blastp/). You can also specify the path using the command line flag -antibody:blastp /my/path |
| 4 | Rosetta Antibody encounters encounters “ BLAST Database error” | The blastp database is not specified, and Rosetta Antibody is not finding it in the default location ( $ROSETTA/tools/antibody/blast_database/) | Specify the grafting database location with -antibody:grafting_database /database/location |
| 4 | Rosetta Antibody produces BLAST output (e.g. grafting/orientation.align) but does not produce structural models (e.g. model.0.pdb) | Your version of BLAST+ may be out of date. | Download a compatible version of BLAST+ (version 2.2.28 or later). See Materials section. |
| 4 | Regular expression failure for CDR identification | Mutations in regions of the chain that Rosetta expects to be conserved prevent the sequence from being split into structural segments correctly. | Check your antibody sequence against the printed regular expression used to detect the CDR. To accommodate unusual sequences, the regular expressions can be altered by changing the file database/protocol_data/antibody/cdr_regex.txt. |
| 17 | SnugDock reports “ERROR: Could not find disulfide partner for residue 23” | A disulfide bond was disrupted during docking. | You can disable disulfide bond detection with the flag -detect_disulf false |
| 17 | SnugDock reports “ERROR: ReturnSidechainMover used with poses of different sequence; aborting” | The structures in the ensemble are not consistent. | Make sure that all sturctures have identical length chains and that if there are multiple chains, those chains appear in a consistent order. |
| 17 | SnugDock reports error “chains are not named correctly or are not in the expected order” | Input PDB does not contain chains in correct order (light, heavy, then antigen) or chain IDs are not L, H, and A. | Adjust chain order in input PDB or specify chain IDs with the –partners AB_C flag, where A, B and C are the light, heavy, and antigen chain IDs, respectively. |
| 2–17 | Other Rosetta errors. | Seek help on the Rosetta forums, www.rosettacommons.org/forum | |
| 2–17 | Common fixes |
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