RSC CICAG Open Source Tools for Chemistry Workshops:- GNINA

[@marawanahmed7829]

Two hours of distilled pure science. Thanks so much David.

[@shehbaz205]

Very Important for me, Thank you RSC_CICAG and whole team

[@MrJeffreynho]

Question: At 1:38:26, there are always two numbers given next to each "Affinity: " followed by "(kcal/mol)". Could you please explain what these numbers are exactly (e.g. : intermolecular/intramolecular/binding energy/Gibbs energy/Kd) and which one actually represents the Affinity? smina, vina (and seemingly gnina) seem to do this whenever --minimize is passed and I've looked everywhere but no documentation about this is readily available. Taking a look at the code, it seems that the first number only represents the INTRAmolecular energy but my i don't know enough C++ to be sure! I've also noticed that generally the lower the first number goes, the higher the second gets, but there doesn't seem to be a linear correlation. Why are there 2 numbers given when it really should be just one? EDIT: Oh, nevermind, i dug into the code a bit more. it seems that the first number is indeed the affinity dG_aff = -RTln(Kd) while the second seems to be the ligand's intramolecular Gibbs free energy dG_ligand it makes sense to have both so the total Gibbs energy of the complex can be derived.

[@mobasserhosain6916]

Outstanding invention. How to perform multiple ligand docking

[@ximingxu1337]

Docking results are often seen in scientific publications. However, many cases with low quality in terms of method details and result evaluation. Some use vina for very flexible ligands, which made vina very tired; some prepapration with add charge, and vina was angry, "I do not need charge!"; I suggest reviewers for docking part should raise questions in ligand strain enery, or torsion penalty, inter or intra clash, key interaction(or key hbonds), pose stability, waters etc.

[@jameelabduljalil25]

Interesting! So how ligands should be prepared for Vina? And how evaluation should be done? Any published literature?