Hi,

After preparing my receptor (DockPrep in Chimera) and my ligand palmitic acid (Add hydrogen and charge in Chimera) I get the following error when I try to use autodock vina.

The protein has a heme-group at the active site and I think that's what causes the error, but I cannot find a solution.

My receptor iis IG455model.pdb

I copied the error message below:

No SEQRES records for IG455model.pdb (#0) chain A; guessing terminii instead

Chain-initial residues that are actual N terminii: #0 MET 1.A

Chain-initial residues that are not actual N terminii:

Chain-final residues that are actual C terminii: #0 PHE 455.A

Chain-final residues that are not actual C terminii:

349 hydrogen bonds

Hydrogens added

Wrote C:\Users\Rasmus Ohrt Johansen\Desktop\Kandidat\10.semester (Master's Thesis)\Modelling and docking for Master Thesis\IG455AutodockVina.receptor.pdb

Traceback (most recent call last):

File "C:\Program Files\Chimera 1.17.1\share\vina\ws.py", line 395, in prepareReceptor

execfile(scriptPath, d)

File "C:\Program Files\Chimera 1.17.1\share\chimeraInit.py", line 209, in execfile

original_execfile(filename, exec_globals, exec_locals)

File "C:\Program Files\Chimera 1.17.1\bin\lib\site-packages\AutoDockTools\Utilities24\prepare_receptor4.py", line 172, in

delete_single_nonstd_residues=delete_single_nonstd_residues)

File "C:\Program Files\Chimera 1.17.1\bin\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 533, in __init__

version=version, delete_single_nonstd_residues=delete_single_nonstd_residues)

File "C:\Program Files\Chimera 1.17.1\bin\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 140, in __init__

self.addCharges(mol, charges_to_add)

File "C:\Program Files\Chimera 1.17.1\bin\lib\site-packages\AutoDockTools\MoleculePreparation.py", line 226, in addCharges

chargeCalculator.addCharges(mol.allAtoms)

File "C:\Program Files\Chimera 1.17.1\bin\lib\site-packages\MolKit\chargeCalculator.py", line 80, in addCharges

babel.assignHybridization(atoms)

File "C:\Program Files\Chimera 1.17.1\bin\lib\site-packages\PyBabel\atomTypes.py", line 127, in assignHybridization

a.babel_atomic_number = self.get_atomic_number(a.babel_type)

File "C:\Program Files\Chimera 1.17.1\bin\lib\site-packages\PyBabel\atomTypes.py", line 103, in get_atomic_number

(name,_name) )

ValueError: Could not find atomic number for Ha Ha

Receptor preparation for AutoDock Vina failed; please look in Reply Log to see error messages.

cannot prepare receptor for AutoDock Vina; please look in Reply Log and/or run Chimera with --debug flag to see errors.

I appreciate you reading this,

Best Rasmus