The Molecular Graphics Laboratory Forum

Dear users

I am Onur Alten from Hacettepe University. I am a master student and i am working about HIV entry inhibitor. And i have used autodock vina program to perform virtual ligand screening. I have some question about my results.
1) I think that my ligand has no interactions with receptor. Do you agree with me or are there any interactions between receptor and ligands? I attach two different output.pdbqt ( two different ligands),receptor.pdbqt file and two different log files .
2) A paper[ (biorganic&medicinal chemistry 16 (2008) 3039-3048 ] says remove one C-helix to expose hydrophobic pocket of 1AIK.pdb . Could you suggest other modifications? I only remove C-chain and after i start docking. Should i make another thing about 1AIK (charges etc...)
3) How can i choose an appropriate grid box for docking ? Should grid box contain both ligand and receptor?
4) Before preparing receptor.pdbqt ,I selected GLN575,GLN577 and ARG579 residue by using select from string options. Is it a true behavior?

My conf.txt files is belove :

receptor = receptor.pdbqt

center_x = 19.468
center_y = 18.666
center_z = 25.827

size_x = 50
size_y = 50
size_z = 60

num_modes = 10

energy_range = 1.1

Best Wishes