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ccsb-scripps / AutoDock4

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Segmentation Fault (core dump) #2

Open hwcopeland opened 1 day ago

hwcopeland commented 1 day ago

Didn't know where to go to next so I figured its time to just open an issue as experts in the use of Autodock4 are few and far between.

For Reference, All files are included in this master repo: https://github.com/Khemiatic-Energistics/compute-infrastructure

Enviorment: Autodock4 is baked into a container running ubuntu 22.04 (compute-infrastructure/docker/autodock4/Dockerfile) and hosts a series of scripts. Each script in Executed with the Kubernetes Operator in an Apache Airflow DAG, in sequenced and batched processing.

Upon final execution of Autodock4, am greeted with Segmentation fault (core dumped)

root@5ac021b5772c:/data# /autodock/autodock4 -p /data/batch0/output/docked/ligand_7.dpf -l /data/batch0/output/docked/ligand_7.dlg -d
Segmentation fault (core dumped)

Image is available with docker pull hwcopeland/auto-docker:latest

attached are dpf and the log

ligand_7.dpf.txt ligand_7.dlg.txt

diogomart commented 1 day ago

Hello, We aren't maintaining autodock4 anymore. The AD4 scoring function is supported in both AutoDock-GPU and AutoDock-Vina (with --scoring ad4) in this organizational account, and the search algorithms are far superior. You could try vina as you'd just need to download an executable, it's far easier to use than autodock4, and might be installable from conda-forge for your system.