Closed linminhtoo closed 1 year ago
I found the problem. It only throws this error if the .pdbqt
file contains multiple poses.
If I read the .pdbqt
and then do some text parsing to retain just the top pose, then it works fine:
from meeko import PDBQTMolecule
with open(my_pdbqt_path, "r") as f:
poses = f.read()
top_pose_pdbqt = "MODE" + poses.split("MODE")[1]
pdbqt_mol = PDBQTMolecule(top_pose_pdbqt, is_dlg=False, skip_typing=True)
rdkit_mol = pdbqt_mol[0].export_rdkit_mol()
So, seems like there's a bug when reading multiple poses?
I also confirm that the below works:
pdbqt_mol = PDBQTMolecule.from_file(my_pdbqt_path, skip_typing=True, poses_to_read=1)
...
Hello
Looks like the program you used (Vina-GPU) writes MODE
instead of MODEL
. So this fixes it:
sed "s/MODE /MODEL /g" results.pdbqt > results-OK.pdbqt
By the way, this molecule is a macrocycle but most likely Vina-GPU can't handle the CG/G pseudo atoms, so it isn't rebuilding the broken bond between CG atoms.
Hello,
I tried to parse
.pdbqt
file usingmeeko
but got an error:Here's the PDBQT file for your reference: https://gist.github.com/linminhtoo/5949437ae066fdd136709971dcc36220 The ligand was prepared using
meeko
before docking to Vina-GPU.Do you know what's the issue? Thank you! Min Htoo