I'm working on a project whereby I want to prove I actually know what I'm doing with ADV, but something is not working out for me. For some reason every time I do a run using my ligand and receptor, and place the grid box deep within the receptor, the ligand is still projected to dock on the outside of the protein. Does anyone have any advice for this? I've attached my files for your consideration. I have verified time and time again that I'm working at 1 angstrom, and the box is where it's supposed to be, which is in a pocked on the 'C' subunit.
Many thanks in advance.
Hi Jonathan,
Can you upload your receptor.pdbqt, ligand.pdbqt, and config.txt files?
Dear Jonathan,
I checked your input files and I think that the problem is your ligand. It has an abnormal geometry. That's why you should add missing atoms via some visualization software (GaussView etc.) and save it as a PDB file. After that, you can upload the ligand into Autodock Tools.
Dear Jonathan,
In addition to Volkan's answer, I suggest removing crystallographic water residues and ligands from your receptor.pdb (5en5.pdb file).
Also, this tutorial might be helpful:
autodock.scripps.edu/faqs-help/tutorial/using-autodock-4-with-autodocktools/2012_ADTtut.pdf
Volkan Fındık Looks like that was a major issue, so thank you for pointing that out. I'm not sure what happened in my initial conversion from one file type to another, but something definitely went wrong.
Amirreza Dowlati Beirami I didn't think there was any water in that structure, but I may have accidentally uploaded the wrong file. I also agree that water will make things wonky.
Thank you both for your input!
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