Dear Christine, Your fist question is regarding range of energy in high affinity. In Autodock Vina high affinity energy varies from -9 to -11 Kcal/mol. In my opinion -4.5 to -3.0 Kcal/mol is moderate affinity for ligand.
Second question is how to save individual orientation of Vina output in pymol. generally i used to open vina output(.pdbqt) in pymol, which contain 9 orientations. I clicked in each orientation and go to file>save molecule in pymol and save our interest of orientation. so you can save 9 orientation in .pdb format. Good luck Chandan --- On Mon, 25/2/13, Harman, Christine <christine.har...@fda.hhs.gov> wrote: From: Harman, Christine <christine.har...@fda.hhs.gov> Subject: [ccp4bb] Autodock Vina output files To: CCP4BB@JISCMAIL.AC.UK Date: Monday, 25 February, 2013, 3:46 PM Hi All, I am sure that some of you have used AutoDock Vina so I thought I would give it a go and ask two questions. I performed a round of docking and obtained an output file containing 9 different models. The affinity (kcal/mol) ranged from -4.5 to -3.0. My first question is what is considered high binding affinity i.e. what range is considered high affinity, moderate affinity etc. My second question is about the output file. The output file is in pdbqt format and can be viewed in Pymol just fine, but the problem is that I cannot separate out the individual orientations of the output file. I want to change the format to pdb so that I can change the depiction of the models in PyMol, but PyMol treats the file as one file and will not allow me to read out the models as separate pdb files. Does anybody know how to separate out the different models contained in one output file provided by AutoDock Vina. Thanks for any advice. Take care, Christine
