Re: Cavity solvation

From: Bill Ross <>
Date: Mon 29 Jan 2001 16:54:04 -0800 (PST)

        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
Before using solvatebox, try solvateshell using WAT instead of
WATBOX216. The problem in filling cavities is that the structure
of bulk water isn't adapted to such spaces - each is very specific.
In either case, you can use the optional 'closeness' parameter to
jam more water in (closer contacts).

Once the cavity is full, use solvatebox to solvate the exterior.

Bill Ross
Received on Mon Jan 29 2001 - 16:54:04 PST
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