Dear all,
I just tried to prepare my receptor for docking with ADT, and it returns error message. However, I did the same thing with same protein(chains A-F) and everything were good. This time I tried to dock my ligand to catalytic domain(chain A+B, used PyMol to extract), but it popep up with ArrtibuteError. I followed the same process - delete waters, add polar hydrogen, and add Kollmann charge, but yielded error. I just want to get the complext and use MD to see how the active pocket collapse upon allosteric ligand binding.
My target is 6MC1, there is a PDB (1zzw) for catalytic domain. I used 1zzw and got error, so I turned to chainA+B of 6MC1(same sequence) instead, but got same error. I have checked the pdb with text, and I did not find missing residues.
I have no idea how to fix it, could anyone please help me with it? Any suggestions are appreciated.
ps: I tried OpenBabel before, but somehow my Vina did not recognize the pdbqt; I cannot open Chimera (both windows and linux)
Looks like a software or software dependency problem. Did your software installation worked earlier with any other molecule or is it the first analysis on a new installation?
Tini Chu Hi
You prepare again your receptor adding polar hydrogen and other charges like (kollman, gasteiger etc ) generate grid file after that dock. dlg
Can you tell me please what changes have you made in settings? I am also facing same issue while saving my pdbqt file of one of my ligand.
Nishat Malik, did you solve this? Having the same problem.
attributeerror: bond instance has no attribute 'leaf'
and
attributeerror: bond instance has no attribute 'activeTors'
I have the same problem, could you tell me the change you made in settings? Tini Chu
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