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 Post subject: covalent grid map.
PostPosted: Wed Jun 29, 2011 9:52 am 
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Joined: Mon Feb 21, 2011 11:50 am
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I tried to set up a covalent docking (autodock 4.2) using a covalent grid map, as done in the paper GM Morris, J Comp Chem 2009, 30, 2785-91.

I can restrict one atom using a Gaussian well, and it works OK. However, I would like to restrict TWO atoms, just as in the paper. Somehow, I cannot figure out how to do this. I couldn't find it in the tutorials. The Autodocktools software only lets me define a 'Z' type atom for one atom on the ligand. How would I restrict a second one? Do I need to change something in the grid parameter file?

Any input on this is very welcome!


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 Post subject: Re: covalent grid map.
PostPosted: Thu Feb 05, 2015 5:44 pm 
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Hi dear,

I would like to find out the procedure you used for restricting a single atom while docking. It is not well explained in the paper i read it from. I will be grateful if you can help. When I click on set covalent map it says the Z atom is unknown.


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