Hello all,
I have been trying to dock a proposed ligand to a structure of a protein I have just solved. I followed a YouTube tutorial and I managed to use AutoGrid just fine. However, when I attempt the actual docking, the docking window shuts after a few seconds and no results are being generated.
Has anyone got any idea regarding what I might be doing wrong? I converted an .sdf ligand file into a PDBQT file and followed the standard procedure for a protein. I am happy to provide my files shall anyone be interested!
Kind regards,
Paulina
Hi Pritam,
Thank you for your suggestions.
I think I have followed all of the steps (I have followed this tutorial: https://www.researchgate.net/post/How_do_I_install_and_run_AutoDock_42_and_AutoDock_Vina) and I still can't get it to work. I have also re-installed MGL tools but it doesn't seem to help at all.
My ligand is beta-ionone and I downloaded an .sdf file and converted it to PDBQT in OpenBabel.
Any suggestions to why AutoGrid would work fine (I get all of the maps etc.) but not AutoDock?
Regards,
Paulina
Hi again,
I think I have sorted it out - my theory is that AutoDock did not like my super long file names!
Once again, thank you for your assistance.
Best,
Paulina
Autodock doesn't detect "spaces" in file-name. Your theory is technically correct.
file conversion maters. use open babel to convert file .first covert the sdf file file into pdb using open babel software, available freely online.
or you can draw the structure freshly and save as pdb and the n convert into pdbqt file using autodock tool only. dlelete all molecule after every step. always open macromolecule and ligand in instead of of choosin. try this i hope it will work
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