Cavity solvation

From: Anton Guliaev <abguliaev_at_lbl.gov>
Date: Mon 29 Jan 2001 15:45:15 -0800

Dear Amber Users -- the protein I am using for MD simulations has a deep
cavity (almost channel), which does not filled with water using the
solvatebox command in xleap. What would be the best way to solvate this
cavity/channel -- The only way I can imagine is to calculate the solvent
accessible surface area and then from equilibrated water box cut the
area of the cavity (how?) -- than combine coordinates (protein and
water) -- though I would expect that it should be an easier way to do
this -- thanks a lot -- Anton

-- 
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        * Anton B. Guliaev, Ph.D           *
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Received on Mon Jan 29 2001 - 15:45:15 PST