HI,
In grid analysis using ptraj option grid,
on visualization of the hydration pattern in vmd, on increasing the
contouring level above 3 times bulk water density presence of hydration
sites decreases,
two hydration sites are observed in the minor groove of DNA on both sides
of the bound ligand at that state. Does that signify something like a high
residence hydration site near the ligand.
I want to know how grid analysis can be usefully interpreted?
thanking you
Mary Varughese
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Received on Tue Jul 01 2014 - 19:30:02 PDT
