I was trying to prepare a ligand for docking with Vina. I have the PDB file, but I am getting an issue with making it a PDBQT file with autodocktools, and the prepare_ligand4.py script.
When I open the ligand .PDB in PyMol, I see an unbroken molecule, but AutoDockTools displays it as missing a C-C bond in the middle of the molecule. This produces a truncated .PDBQT file. How can I get AutoDockTools or prepare_ligand4.py to correctly read the file? I've tried the -A bonds_hydrogen option with no success.
The PDB file for the ligand is as follows.
Code:
HETATM 4702 O2 MCO A 702 38.698 33.169 41.883 1.00 17.26 O
HETATM 4703 C9 MCO A 702 39.916 33.427 42.273 1.00 19.68 C
HETATM 4704 O3 MCO A 702 40.403 32.352 42.793 1.00 18.43 O
HETATM 4705 C8 MCO A 702 40.848 34.344 42.347 1.00 21.41 C
HETATM 4706 C7 MCO A 702 41.480 34.830 41.034 1.00 20.72 C
HETATM 4707 C6 MCO A 702 42.829 35.194 41.508 1.00 23.73 C
HETATM 4708 C5 MCO A 702 42.376 35.775 42.848 1.00 20.15 C
HETATM 4709 N MCO A 702 41.351 34.887 43.471 1.00 21.18 N
HETATM 4710 C4 MCO A 702 41.014 34.687 44.754 1.00 20.08 C
HETATM 4711 O1 MCO A 702 39.872 34.401 45.087 1.00 19.41 O
HETATM 4712 C2 MCO A 702 42.478 34.953 45.617 1.00 20.72 C
HETATM 4713 C3 MCO A 702 42.961 33.931 45.860 1.00 19.99 C
HETATM 4714 C1 MCO A 702 41.994 35.764 46.827 1.00 21.36 C
HETATM 4715 S MCO A 702 42.973 36.411 48.179 1.00 24.81 S
The PDBQT file produced by prepare_ligand4.py is
Code:
REMARK 3 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: C9_2 and C8_4
REMARK 2 A between atoms: N_8 and C4_9
REMARK 3 A between atoms: C2_11 and C1_13
ROOT
HETATM 1 C2 MCO A 702 42.478 34.953 45.617 1.00 20.72 -0.003 C
HETATM 2 C3 MCO A 702 42.961 33.931 45.860 1.00 19.99 0.011 C
ENDROOT
BRANCH 1 3
HETATM 3 C1 MCO A 702 41.994 35.764 46.827 1.00 21.36 0.056 C
HETATM 4 S MCO A 702 42.973 36.411 48.179 1.00 24.81 -0.065 SA
ENDBRANCH 1 3
TORSDOF 3
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