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PostPosted: Tue Feb 05, 2013 7:54 pm 
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Joined: Tue Jan 15, 2013 9:30 am
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I modified VINA source code and now I can do detailed interaction studies such as in the attached picture; this is cyclodextrin and some ligand. In the ligand, red spheres indicate atoms that make hydrogen bonds and white spheres indicate strong hydrophobic interactions; radius of each sphere is proportional to the absolute value of the interaction.

In this case it seems to me that "radius" for hydrophobic interactions is too smal; because double bonds on pterostilbene do not get hydrophobic stabilization as it should be. So my question is; is it possible, tweaking sorce code, to increment this "radius"?


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