Unfortunately the surface area commands in CPPTRAJ won't partition the
surface areas into hydrophobic/hydrophilic components.
-Dan
On Fri, Jul 29, 2016 at 5:50 PM, anu chandra <anu80125.gmail.com> wrote:
> Dear Amber users,
>
> I am working with protein-ligand system and I am trying to calculate how
> much of hydrophobic surface area (excluding hydrophilic area, if any) of
> ligand is exposed to water during the simulation. I am aware of the 'surf'
> and 'molsurf' tools in CPPTRAJ. I just wonder whether any of these can be
> exclusively used to calculate the hydrophobic region of ligand exposed to
> surrounding water environment.
>
>
> Many thanks in advance
>
> Anu
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Jul 29 2016 - 19:30:03 PDT
