Initial pose not within the box; ligand outside the box

gnina / gnina

A deep learning framework for molecular docking

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Initial pose not within the box; ligand outside the box #261

Open ngran1 opened 2 months ago

ngran1 commented 2 months ago

Issue summary

Hi, I am trying to use GNINA for docking of macrocycles. However no matter if I use autobot_lig command and after the ligand extracted from the protein, or I enter xyz coordinates extracted from Maestro, I get this:

Screenshot 2024-05-29 at 11 58 37

what is even more odd is that I get results, but unfortunately when I preform rmsd (since I am redocking the ligand) the RMSD is bad.

How can I solve this?

Thanks

dkoes commented 2 months ago

Perhaps your box is not big enough (your reference ligand is smaller than the ligand being docked) or the box is in the wrong place. Try increasing autobox_add, but also visually verify that lig.pdb is in the right place.