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PostPosted: Wed Mar 04, 2015 9:45 pm 
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Hi,
I am trying to understand the meaning of the electrostatic and desolvation maps created by Autogrid4; my understanding so far is these maps are dependent only on the receptor rather than the ligand as well. I read here (https://web.njit.edu/all_topics/Prog_La ... Guide.html) that the electrostatic one is giving the coulombic interactions due to the target atoms acting on one probe charge; why Autodock need that map? On the other way, I have difficulties in understanding how the desolvation map is calculated; again, I read in this webpage (http://autodock.scripps.edu/resources/s ... ree-energy) that there are two separate terms (deltaG, precalc and deltaG, lig) and the first one is precalculated regardless the ligand (I assume this is the desolvation map hat Autogrid produce, containing the desolvation result on each point of the grid), however it seems to me that the equation still need to know the atomic solvation parameter and fragmental volume for atoms of the ligand, thus I cannot understand why this map is the same for the same structure regardless the ligands; moreover, the page talks also about this deltaG, ligmap that is used for calculating the deltaG, lig for each atoms; where is this map? I could guess that this ligand-dependent desolvation contribution is already included in each point of the atomic affinity maps. Thanks in advance for your help,

Francesco


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PostPosted: Mon Mar 16, 2015 7:21 pm 
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The electrostatic and desolvation maps autogrid4 generates based on the rigid portions
of the receptor speed up autodock4 by facilitating the use of tri-linear interpolation
for computing these energy components.
Tri-linear interpolation is faster than re-calculating each energy between a moving
atom in the ligand and every rigid atom in the receptor.


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