Urgent: Stuck jobs in queue and water refinement (itw) - HIV-1 Tat/Receptor docking

HADDOCK
,
1

Dear HADDOCK Support Team,

I am an MD-PhD student conducting in silico research on HIV-1 Tat structural variants. I currently have six (6) active docking jobs that have stalled significantly at different stages of the pipeline, preventing me from concluding my thermodynamic analysis:

Jobs stuck at water refinement (itw) for >24 hours:

  • 692444

  • 692448

  • 692452

Jobs still stuck in the initial queue for >24 hours:

  • 692446

  • 692450

  • 692453

Project Details:

  • Target: HIV-1 Tat Exon 1 / human NMDA or hDAT complexes.

  • Issue: Half of the jobs progressed/are progressing through it0 and it1 normally (albeit these runs are relatively slower than my usual jobs before at HADDOCK 2.4), but have been stalled at 0.0% in the water refinement (itw) phase. The other half have not yet been initialized despite being submitted at around the same time.

These simulations are critical for the thermodynamic analysis required for my PhD research. Could you please investigate if these jobs have stalled on specific worker nodes? If it is not possible to resume them, please let me know so I can clone them and resubmit, or if there is any server-side bottleneck I should be aware of.

Thank you very much for your time and for maintaining this essential resource.

Best regards,

--

Sincerely,

SHAUGHN

2

Because of the size of your systems the runs are redirected to a local long queue, which has less resources…

Be patient, and/or try to minimise the system size (e.g. by removing unneeded parts of your proteins if you know where the binding sites are).

Remember you are using free resources :slight_smile: