I've a receptor and ligand both as pdb file. With mgltools I've converted them to pdbqt. Then performed docking with autodock vina. Now I want my receptor and pdbqt generated by vina to have in a single file. Is it possible?
very simple you can use Chimera tool
Auto dock vina result in chimera
Open Chimera
Step 1) Go to File - Open you receptor file in .pdb format (receptor protein is loaded).
Step 2) Go to Tool Surface / Binding Analysis View Dock.
Step 3) Select your ligand_out.pdbqt file this (ligand is loaded in you receptor file) & (will add a new window for ligand poses)
Step 4) Go to Tool Surface / Binding Analysis FindHBond
Step 5) Select which ligand pose is optimum with respect to the active site and energy.
Step 6) File save pdb (new saving window will be loaded
File type PDB (.pdb)
Save models receptor.pdb (#0)
(#1.1) ligand pose
(#1.2) ligand pose
(#1.3) ligand pose
(#1.4) ligand pose
Select receptor.pdb and with the help of ctrl select the ligand pose one at time for individual complex.
Example:
receptor.pdb (#0)
(#1.1) ligand pose
Save == complex-model1.pdb
Yes, with mgltools you can open those files and then select them in the dashboard and you click (right button) "Current selection" and "Split"
I always save the ligand pdb file from docking log file. And then run cat receptor.pdb ligand.pdb > complex.pdb in Linux or Mac. In windows, you have to combine them manually.
very simple you can use Chimera tool
Auto dock vina result in chimera
Open Chimera
Step 1) Go to File - Open you receptor file in .pdb format (receptor protein is loaded).
Step 2) Go to Tool Surface / Binding Analysis View Dock.
Step 3) Select your ligand_out.pdbqt file this (ligand is loaded in you receptor file) & (will add a new window for ligand poses)
Step 4) Go to Tool Surface / Binding Analysis FindHBond
Step 5) Select which ligand pose is optimum with respect to the active site and energy.
Step 6) File save pdb (new saving window will be loaded
File type PDB (.pdb)
Save models receptor.pdb (#0)
(#1.1) ligand pose
(#1.2) ligand pose
(#1.3) ligand pose
(#1.4) ligand pose
Select receptor.pdb and with the help of ctrl select the ligand pose one at time for individual complex.
Example:
receptor.pdb (#0)
(#1.1) ligand pose
Save == complex-model1.pdb
you can do by copying the coordiantes of the best pose from autodock vina to the protein receptor file..
open the out.pdbqt
From model 1-Copy from "ROOT" to TER
paste tit at the end of receptor file and save it in .rtf format
open in chimera and save it as .pdb
Hello Ruhshan!
I hope Mr. Pramodkumar P Gupta response may HELP you. Here, I wish to share a method to combine the ligand (minimum energy conformer) with their docked receptor file. While performing the AutoDock Vina, you have get the final output 'filename.pdbqt' of the all conformational positions of your ligand.
Vina_Split program has HELPful to separate the confermers from the AutoDock Vina output file 'filename'.pdbqt
STEP: 1 Sperate the each conformers from the final 'out.pdbqt' file
cmd comment: vina_split --input filename.pdbqt
STEP: 2 Combine the separated conformer-1 (Minimum energy) with the receptor .pdb file
Copy the 'filename_ligand_01.pdbqt' file and paste at the end of the receptor .pdb file
I hope it's HELP (see the video)
https://www.youtube.com/watch?v=DiF7LxHrmSo
Thanks
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