Thank you so much for the video tutorial. I have a questions: if a protein have two chains (chain A and B), for example BCL-2 with PDB entry 2W3L (Crystal Structure of Chimaeric Bcl2-xL and Phenyl Tetrahydroisoquinoline Amide Complex) and my target is Phenyl Tetrahydroisoquinoline Amide Complex. How we know Phenyl Tetrahydroisoquinoline Amide Complex in which chain? Please help
I know site-specific is a lot more efficient and faster than random docking, but I would still like to learn random docking protocols in case I'm facing a completely novel protein structure?
UGH - frustrating - spent all afternoon setting up my programs, then my pdbqt files, then when I run the docking from terminal I get this: -bash: vina: command not found Any help?! Ready to smash something, lol!
Hi, I followed the same steps but when I visualize the ligand in PyMOL I have only one state even if Vina has generated 8 models. I checked the pdbqt ligand file on a txt editor and in Autodock tools and it has actually 8 models inside. How come PyMOL visualizes only one of them? many thanks for your answer!
How to delete hetatoms and other chains while keeping only one chain? Also, the file you got after clicking on download > PDB format, is different from what I got. I only got the 3D structure of protein which after clicking on it gets opened directly in pymol. How to download the file which you are showing the video?
Maam mere binding energy pyrx virtual tool se -12.2kcal/mol aare h , but DSV se result analyse krne m unfavourable bumps, alkyl, vandevall interaction aese show hore hain.... To sir kya ye galat hai
How did you just randomly have a configuration file, should have been explained early in the video. Not many articles are mind enough to provide as in depth information as that
Are blind docking using Auto dock vina and then visualisation by pyMOL sufficient for new synthesized compounds? (About synthesis oriented research) Please suggest mam
Hi, thank you for your video but I am facing an issue. I am using windows and with the command you provided, it is not reading the config file. It is showing vacant every time.
my protein doesnot contain cl atom which is there in the ligand and maps are generated for all atoms in the protein. while autodocking its showing the error: I'm sorry; I can't find or open "@t" the atoms in protein are : A C H HD N OA SA and atoms in ligand are:A Cl OA N pls tell how remove the error
I have a doubt. HETATM also represent water molecules. So, if i am removing it manually via text editor, then the step of removing water molecules via autodock is not required. Right?
Hello mam, I am trying to perform site specific docking as per ur procedure on windows using vina but the problem is that instead of docking with my selected residues the ligand combine with other residues in the grid box, I tried many times but failed due to this my result obtained is not as expected . So pls tell me the solution for this. Thank u!
Everything was going good until 10:55 - then the train absolutely fell off the track 😂WTH happened? And here I thought I actually could do docking... SMDH
It might be helpful to briefly learn how to use command lines. Autodock Tools just preps you with pdbqt files and setting up configurations, but the actual Vina part is run on the command line. All you need to learn about command line is how to locate your files (cd) and make sure you downloaded vina properly, which differ by the OS you use.