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PostPosted: Tue Mar 03, 2015 2:00 am 
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Joined: Tue Mar 03, 2015 1:46 am
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Hi, I have a question regarding the precalculations made by Autogrid. I understand that for each atom in the ligand an affinity map, containing the potential due to the interactions with the target, is computed. However I don't get well the concept of desolvation and electrostatic maps:
1) these two maps are not dependent on the type of ligand atoms specified in .gpf file, so I can guess that the electrostatic one is calculated as the potential due to all the protein atoms on a probe charge in each point of the grid; what is the utility of doing that?
2) after taking a look on http://autodock.scripps.edu/resources/s ... ree-energy I see that basically the desolvation term is broken in two parts; the one called deltaG,precalc is supposed to be calculated without knowing the ligand atoms (am I correct by guessing this is effectively the desolvation map given from autogrid?), however in the equation there are still terms regarding the ligand (e.g. ai and Vi); how these parameters are considered if the map is only depending on the receptor atoms?
3) regarding deltaG,desolv,lig (again in http://autodock.scripps.edu/resources/s ... ree-energy), is this part calculated and included in each atom affinity map? The page says that during the docking, when we know the charges we can finally calculate that, but I guess we know the charges on each ligand atom even before running autogrid and so the program should include that on the atomic potential in each grid point, is that correct?
Thanks in advance to all of you


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