Hello. While looking for such a tool on the web, I came across some
references in an old amber list post (I mean, quite old, from 2005 i
think). The post said something about a program written to analyse such
hydrogen bonded water networks. Here is the link I found:
http://www.geocities.ws/dviip/menu.html
I am guessing that this tool no longer has any support, but it would be
nice to find something similar that is currently working.
Thank you
Fabrício
2013/7/11 Daniel Roe <daniel.r.roe.gmail.com>
> Hi,
>
> On Thu, Jul 11, 2013 at 5:09 PM, Fabrício Bracht <fabracht1.gmail.com>
> wrote:
> > between residues. Does hbond identify if two residues are bridged by more
> > than one water molecule, i.e., an interaction of the type "RES1 - WAT -
> WAT
> > - RES2" ?
>
> No, currently the code looks for single bridging water molecules only.
> As you can imagine the book-keeping becomes much more complicated when
> you consider 2+ bridging molecules (since now you have to look at all
> solvent-solvent hbonds as well). I wouldn't rule putting this
> functionality in at some point, but it's complicated enough that it
> likely won't be available in the immediate future.
>
> -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) 585-9119 (Fax)
>
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Received on Thu Jul 11 2013 - 17:00:03 PDT
