the protein i am working on is HPV16 E6 ID : 4xr8 chain H . It contains 2 zinc atoms that are important as they form zinc finger. i Manually edited pdb file in column 79,80 and add 2+ to both Zn atoms. However, after preparing protein pdbqt file using auto dock tools , message show up saying there are zero charge on theses atoms Zn Zn . I ignored the message but after selecting the binding site residues and
flexible residues >>> input>>> choose macromolecule then
flexible residues >>> choose torsions in currently selected residues
flexible residues >>>output>>> save flexible pdbqt
an error "Sorry, there are no Gasteiger parameters available for atom E6_CHAIN_H:H: ZN201:ZN"
appeared.
Ricardo J Ferreira
Hi, I have aleardy done that before and no error message has shown up. However, when I started docking of aligand to the protein using supercomputer, an error appeared saying that there is apriblem with line ## that an atom should not been there.
l may have added the charge incorrectly. Could you please till me where exactly i can edit the charge value in pdbqt file ?
Thanks
AutoDock forcefield was not parameterized to included metals such as Zn, so care must be taken when trying to generate poses for ligands with these metals in the binding site. If you want to be rigorous, you should generate the charges by means of QM and recalibrate the forcefield. But there are suggestions by the same authors:
http://autodock.scripps.edu/faqs-help/how-to/adding-new-atom-parameters-to-autodock
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