I have performed molecular docking and found 9th conformation is the best for me as it has the minimum amount of binding energy. Now I want to save it for using later analysis in BioVia Discovery Studio to generate 2d plot. Now when I open my pdbqt file in discovery studio, it is showing all the 10 ligands which I don't one. I want the ligand responsible for 9th conformation.
How can I proceed further to generate a 2d plot showing interactions for the 9th conformation?
Thanks in advance
Hello,
Open the receiver in pdbqt format in Discovery,Now bring your ninth conformation with the least energy to Discovery,Then save the complex, Discovery saves in pdf format,You can from the Receptor-ligand interaction option, on the left, click the show to diagram option and see the connection links with the ligand, and ...
I filmed for you, please watch.
Open the .pdbqt file of protein in PyMol. Next, open the output .pdbqt file of ligand in PyMol as well. Select the state from the bottom right corner of the PyMol window (9th state in your case). Go to file, export molecule (Selection: all, State: current), and save it in .pdb format. Next, open the saved file in Discovery studio, click on Receptor-Ligand interactions & Show 2D diagram.
@Mr. Tusar Chakraborty , I have used AutoDock 4.2 not AutoDock Vina, so output file is not available.
From the analyze dropdown, click on dockings and open the .dlg file. Next go to analyze, select macromolecule (OPEN). Again from the analyze dropdown, go to conformations and click PLAY. This opens a panel window. Then select the conformation you want (9th in your case). Click on the 2nd last button on the panel window (SET PLAY OPTIONS). Click on write complex and save it in .pdb format. Open this file in Discovery studio and click on Show 2D diagram.
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