AMBER Archive (2001)

Subject: Cavity solvation

From: Anton Guliaev (abguliaev_at_lbl.gov)
Date: Mon Jan 29 2001 - 17:45:15 CST

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 

-- 
        ************************************
        * Anton B. Guliaev, Ph.D           *
      _ * Life Sciences Division           * _   
     / )* LBNL, Berkeley CA 94720          *( \
    / / * abguliaev_at_lbl.gov                * \ \
  _( (_ * T: 510-486-5773 F:(510)-486-6488 *  ) )_
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