I am running the protocol from here https://github.com/LPDI-EPFL/RosettaSurf/tree/main/scripts/interleukin_benchmark. The .xml script works fine however I keep getting the following error at the end:
core.scoring.sc.ElectrostaticComplementarityCalculator: Ignoring atoms farther than 20 from interface.
core.scoring.sc.ElectrostaticComplementarityCalculator: Trimmed 12133 dots to 487 dots.
core.scoring.PoissonBoltzmannPotential: PB_XK8PX9QS.pqr is successfully written.
core.scoring.PoissonBoltzmannPotential: PB_XK8PX9QS.in is successfully written.
core.scoring.PoissonBoltzmannPotential: APBS failed to generate the result file. Terminating the program.
protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing procotol:
[ ERROR ] UtilityExitException
ERROR: APBS failed to generate the result file.
protocols.jd2.JobDistributor: [ ERROR ]
[ERROR] Exception caught by JobDistributor for job 6m0j_AE_9A
protocols.jd2.JobDistributor: [ WARNING ] 6m0j_AE_9A reported failure and will NOT retry
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 623 seconds
I was in contact with the first author from the protocol and he suggested that there might be unrecognized atoms causing errors for the APBS calculation and to use the clean_pdb python script on my structure. I did that and the same error is persisting.
Does anyone have any ideas? I am using the rosetta scripts static release if that changes anything.