ERROR: APBS failed to generate the result file.

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    • #3888
      Anonymous

        Hello all,

        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:

        File: src/core/scoring/PoissonBoltzmannPotential.cc:312

        [ 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. 

      • #16092
        Anonymous

          Does anyone have any idea? 

          [FILE]: src/core/scoring/PoissonBoltzmannPotential.cc

          [LINE]: 306

          [START_MESSAGE]

          [ ERROR ] UtilityExitException

          ERROR: APBS failed to generate the result file.

           

          The error file has:

          sh: apbs: command not found

          ERROR: APBS failed to generate the result file.

          ERROR:: Exit from: src/core/scoring/PoissonBoltzmannPotential.cc line: 306

          [ ERROR ]: Caught exception:

          File: src/core/scoring/PoissonBoltzmannPotential.cc:306

          [ ERROR ] UtilityExitException

          ERROR: APBS failed to generate the result file.

           

           

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