Hi Thripthi, I would suggest that you check a few things:
- when defining the gridbox coordinates, did you set the spacing to 1? - did you properly prepare your receptor (remove bound ligands, ions, waters, adding missing residues to your structure etc) and add polar hydrogens? - did you convert your receptor structure to the pdbqt format? - did you properly prepare your ligands? - you can use a control compound (known binder) for your protein and see if using the same general procedure, you still get a positive score It is possible that you have very bad binders in the end, but generally a positive vina score indicates some problem with the setup. Hope this helps and please let me know how things went Kind regards, Sorin On Wed, Mar 27, 2024 at 11:54 PM Thripthi Shenoy <thripthishe...@gmail.com> wrote: > Greetings to all! > > I have docked a few compounds with a protein using AutoDock Vina. The > compounds are exhibiting positive binding energies even though they are > docked in the active site. I would be grateful for any help regarding the > same. > > Thank you, > Regards, > Thripthi. > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
