Hi Everyone. I'm currently using the DockingApp, a gui for AutoDock Vina. It's an awesome gui and it's worked great for my colleagues. I'm trying to dock a derivative of my ligand into it's specific receptor complex. I can get a decent output (probable binding outcomes), except my ligand is reduced (this really messes up some potential interactions with that part of the ligand and another part of the receptor). I believe my main issue is with my ligand PDB file that I made from scratch using MarvinSketch. I simply copied and pasted a smiles file of my ligand into MarvinSketch, added the extra bit (to make it the derivative) and saved as .pdb. I know that the AutoDock Vina program has an autoreduce program that reduces the receptor PDB and it apparently reduces the ligand pdb too. That completely changes my results. I don't need my ligand reduced, I need it in it's oxidized state.
Is this a super simple problem to fix? Can I not use MarvinSketch to make a proper PDB file for docking simulations studies?
Have any suggestions on how to make a proper PDB file of a ligand?
Thanks for all your help!