I would like to know where I go wrong with my ligand preparation in AutoDock.
The complex compound (with one invisible bond) was optimized in Gaussian 09 and written as * mol2 (Sybyl).
Then, in AutoDock, I added polar hydrogens and detected a root ( torsion tree) .
I wrote the prepared molecule as * pdbqt. After opening it, I only have a part of the whole molecule, broken at the site of "invisible binding". How can I write a whole molecule as * pdbqt?
Here is a tricky way,
pdbqt file is just a pdb file with partial charges("q") and atom types("t"). Since you have the partial charges in a sybyl mol2 format, then you just need to add these autodock style atom types manually. (with a text editor)
Probably Autodock defines the rest as non-bonded atoms so they are excluded in your output. You can upload either your mol2 file and autodock shell output to detect the problem here.
I do not know if that will help you but for docking I simply used openbabel to add hyddrogens to my ligands as well as convert them to pdbqt. It works like this:
obabel -imol2 Name.mol2 -opdbqt -OName.pdbqt -h
I do not know about the root of the torison tree (isn't the ligand static in auto dock ?). You can of course also try to generate multiple conformers with openbabel ( https://openbabel.readthedocs.io/en/latest/3DStructureGen/multipleconformers.html ) and dock them individually.
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