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
