Hi everyone, I am using Autodock and I'm fairly new and unskilled in it. I was performing a protein-ligand dock. I prepared the protein and ligand, saved them in pdbqt, prepared the gpf file and set the autogrind.exe and parameter file for running autogrid. But when I click on launch, it doesnt generate the glg and map files.
I'm not sure if this is of context but when I choose my ligand to set map types, it shows me a warning and a python shell errow, both of which I have attached below,
What should I do? Can anyone help me?
For some reason you have a charge value which is not an integer. Does this protein contain any metals? In general, metals require special handling in docking and MD programs to set the proper parameters. Even if the charges are not an integer, I'm pretty sure you should still get an output file though.
I'm not sure about the Python error, but it seems there is an issue with the specified residue and maybe the atom type on nitrogen. This is probably what is preventing you from getting an output. Have you examined this in your input file?
I'm pretty sure the ussue is not with the protein since I've been using this protein for other docking projects too, and didn't face this issue. I was successfully able to generate a glg and a dlg file both. Therefore I think the issue lies in the ligand. But I downloaded the ligand structure directly from pubchem so I hardly think there's any structural there too.
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