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PostPosted: Mon Jun 04, 2012 1:19 pm 
Millimolar User
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Joined: Mon Jun 04, 2012 12:40 pm
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Hi all,

I am a new user to autodock and as a result feel kind of lost regarding grid generation. From what I have gathered from the online tutorials, there is a focus on docking the co-crystallised ligand back into the enzyme which is straightforward enough. However, for a different ligand, such as a potential inhibitor, when I try to load the ligand file (pdbqt format) and attempt to generate the receptor grid, I can not select the grid that will encompass both ligand and the enzyme's active site. From my experience with Schrodinger Glide, the receptor grid is only generated once and its co-ordinates are specified in the receptor grid file and can be loaded up again when a new ligand is docked. But for autodock, it seems that every time a new grid needs to be generated. How can I generate a grid then for ligand that is not the original co-crystallised ligand then?

Sorry if I totally miss the point, I have tried to look through the entire forum but did not find the answer to my rather simple question? Any help is really appreciated.

Thanks in advance!

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