Automated my docking results by using script

Question

[iamsmor]

Hello everyone

For my project I did many docking with three ligand to proteins via Autodock vina tool. And I got results as output pdbqt and I convert them to pdb as I learn pdbqt not applicable for DSV. Can anyone help me how can I automated docking results for visualization I mainly focus creating 2d diagram ligand-receptor interaction so I have same protocols for all results .

Thank you for any kind

Answer 1

[dthorbur]

There is an existing post with a solution for converting pdbqt to pdb format.

Regarding the visualisation, batch emitting images from something like PyMol module in python is a pretty standard operation. I would suggest learning some PyMol programming.

• https://pymolwiki.org/index.php/Main_Page

You can write a script to emit a 2D image, spin the complex in PyMol, emit another, etc... and then use something like montage to put them all into a single image.