Hello everyone!
I am redesigning the specificity of a protein and make it interact with a DNA sequence. I am trying to run the RosettaDNA application program based on the demos. However, I am getting this error.
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 89 in file myfile.pdb. Best match rsd_type: ADE:UpperDNA
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LYS:CtermProteinFull 59
The PDBfile that I am using is a docked protein-DNA complex (prepared using HADDOCK). The arg file and script file are attached for your reference. Can you please help me to troubleshoot?
| Attachment | Size |
|---|---|
 Arg file | 627 bytes |
| rosettascript file | 1.72 KB |
Category:
Post Situation:
That's just a warning, not an error. Rosetta expects protein chain endings to have a carboxylate form. If you don't have the OXT atom on the residue, Rosetta will put it on for you. The message is just letting you know that it's doing so, in case you were expecting there to already be an OXT atom there (or if you weren't expecting the indicated residues to be a chain ending.) If you're coming from a program which doesn't care about chain endings (or which explicitly removes them), then there isn't any issues -- Rosetta will add back on the OXT atom in the inferred geometry, and then carry on with the protocol.
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 89 in file cluster1_1_trim.pdb. Best match rsd_type: ADE:UpperDNA
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LYS:CtermProteinFull 59
The run is getting discontinued after this message. Can help to fix this issue?
The run shouldn't be stopping due to that message. If it's erroring out, it's erroring out due to some other issue.
What could be happening, if you're redirecting the output to a file, is that there are additional messages which contain the actual error message which get output, but don't actually make it to the file because the output buffer gets dumped when the program exits.
Try running the command directly on the command line, with the output going directly to the terminal, rather than redirecting it. That should let you capture as much of the tracer output as possible prior to the program exiting.
The other thing to look for is a ROSETTA_CRASH.log file in the running directory. In most cases of exiting after error, Rosetta will write that file with a bunch of diagnostic information which may be helpful in tracking down what the issue is.
The other thing to look for is error messages and logs from whatever system you're using to run the program. If you're launching things with an HPC queueing system (e.g. SLURM, Conda, PBS), they'll sometime report error messages or reasons why they canceled the program externally (e.g. ran too long, used too much memory) in a separate log file. If you have one of those, what it says may help in figuring out what's wrong.