Segmentation fault when docking huge MOF-DNA with small ligand

PKUGaoGroup / DSDP

Deep Site and Docking Pose (DSDP) is a blind docking strategy accelerated by GPUs, developed by Gao Group. For the site prediction part, several modifications are introduced to PUResNet program. The pose sampling part is similar as AutoDock Vina combined with a number of modifications.

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Segmentation fault when docking huge MOF-DNA with small ligand #5

Closed supernova4869 closed 1 year ago

supernova4869 commented 1 year ago

I tried to dock a big molecule MIL53-Fe-aptamer complex and a small oxytetracycline molecule with DSDP redocking toolkit, which reported segmentation fault with no other information. Wishing that the reason could be found, thank you! The command is:

/path/to/DSDP/DSDP_redocking/DSDP --ligand OTC.mol2 --protein MIL_apt_3p_oct.pdbqt --box_min 78.868044 61.657419 86.501169 --box_max 116.995082 99.784457 124.628207 --out 3p_oct.pdbqt --log 3p_oct.log

The related files are as below: files.zip

HCAya commented 1 year ago

Please provide a .pdbqt formatted ligand input. The current DSDP_redocking version does not support mol2.

supernova4869 commented 1 year ago

Oh, sorry. I forgot the ligand should also be treated as pdbqt.