Hi,
On Fri, Feb 28, 2014 at 8:05 AM, Alessandra Lacetera <
alessandra.lacetera.gmail.com> wrote:
> Is there any change to find the bridge waters which are between the ligand
> and receptor?
>
Not directly, but I think you should be able to post-process the output
from bridgeout to get what you want. The output looks like:
#Bridging Solute Residues:
Bridge Res 10:THR 11:TRP , 5 frames.
Bridge Res 5:GLU 12:LYS , 4 frames.
...
The residues being bridged are always in order. You can e.g. 'grep' out the
lines containing any ligand residues; this will give you lines containing
residue numbers involved in bridging. Then you could use something like the
'closest' command to isolate waters that are near those residues; among
these will be the bridging waters.
Hope this helps,
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
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 Mon Mar 03 2014 - 08:00:03 PST
