I follow the protocol in this paper "Computational protein–ligand docking and virtual drug screening with the AutoDock suite" for the "Flexible Docking". Everything is smooth until I write the command in Command Prompt, it warns that "the Atom number 19 in the Flexible Residue has not been found"
Please help, what can I do now?
From the screenshot, all I can guess is there are different atoms between your rigid receptor and flexible receptor.
Please make sure that you:
1. Added atoms necessary for both receptors (maybe you forgot to add hydrogens atoms in one of the files?)
2. Deleted all molecules in the same steps (did you forgot to delete some part of the protein in one of the files?)
That is all I can think from that.
If you still unsure, maybe uploading your pdbqt files can help us to check the problem more.
Kindly protein preparation step repeat may be you have midsing something
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