I am performing docking with a single protein and various ligands. So should I be performing autogrid each and every time and for each and every ligand? It just seems not so meaningful. For me as per my understanding autogrid is a program which precalculates grid maps of interaction energies. Please justify my understanding.
Yes, you are absolutely correct. Check this tutorial page 18 (http://autodock.scripps.edu/faqs-help/tutorial/using-autodock4-for-virtual-screening/UsingAutoDock4forVirtualScreening_v4.pdf).
All you need to do is creating & collecting the grid maps for all kind of atoms in all ligands. Just to be sure, perhaps you can use ADT to create gpf configuration file and check how many kind of atomtype are there.
Hope that help,
Radif
hi,
I am aslo having the doubt.
If the receptor and binding site are same for a set of ligands, is there any need of running autogrid everytime?
instead of running autogrid everytime, can we copy those map files and paste in the folder were the next ligand for docking is present?
Hi Sajin,
There is no need to, because Autogrid only require information about the atom types of protein & ligand, and also the structure of the protein itself (check the gpf file). So it is not a ligand-structure specific problem, and thus the map grid can be used for any kind of ligands as long as the atom type conform. Including the desolvation & electrostatic map, because it is protein specific map, not based on the ligand structure.
Hope that can clear some issue.
Radif
Yes. I have found out that auto grid calculations would not require ligand.pdbqt in the working folder. The program writes energy maps for protein and don't require a ligand presence
Grid is just a different kind of protein structure representation. Usually, it includes only the part of the protein containing the ligand-binding pocket (although including the whole protein is not formally precluded). The format is optimized for the docking performance. Obviously, it needs to be generated only once (unless you'd like to change the grid parameters).
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