I have following doubts in the analysis part:
1) In Autodock vina, output file is generated. Theoretically, a complex should form after docking which is represented by the output file. Then, on visualizing the output file, i should be able to see the complex that contains atoms of ligands and receptor. Instead, the receptor file has to be loaded in order to visualize the poses. Why is that?
The output files only contain the variable parts of the simulation (e.g. the docked molecule), and that's all they should contain. Given today's hard drive space, I suppose you COULD paste the protein into each file, but it would still be a waste of time and space since it'd be the exact same data for every file. The only parts of the protein that should be included in the output pdbqt are residues which you specified as flexible (which hopefully would NOT be the entire protein).
You can use software such as Discovery studio visualizer to create a complex of protein and the output ligand.
Link: http://media.accelrys.com/downloads/visualizer/2019/biovia_2019.ds2019client.exe
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