I was trying to prepare the ligand-binding domain of human estrogen receptor beta (1QKM: https://www.rcsb.org/structure/1QKM ) for docking and met the following error on the stage of .pdbqt file generation:

IDLE 1.2.6 ==== No Subprocess ====

>>> Unable to assign HAD type to atom N

Unable to assign valence to atom 1qkm_wo_non_std_rsdus(2):A:PRO358:N type = N

charges on carbons unchanged

Exception in Tkinter callback

The entire text of the error message is attached.

I'm using MGLTools version 1.5.6.

Before the .pdbqt file generation, I removed all Non-Standart residues using ChimeraX software and removed O@A and O@B atoms from Asp359 residue at the stage of hydrogens adding since they were non-bounded.

Does somebody know what it means and how to fix it?

I appreciate any tips and suggestions!

Thank you.