Hi,
On Thu, Jun 25, 2015 at 12:35 AM, DEBOSTUTI GHOSHDASTIDAR <
debostutighosh.gmail.com> wrote:
> Thanks for your response. I wanted to calculate water that bridges between
> two ions.
What you want then is something like:
hbond A_W1 :A solventdonor :WAT solventacceptor :WAT.O \
dist 3.5 angle 135.0 bridgeout watbridge1.dat
Here the "solute" will be the ions.
Hope this helps,
-Dan
> So specified water under solventdonor and solventacceptor and
> ions separately in another mask.
>
> Nevertheless, I tried putting the ion and water under the same mask as
> follows:
>
> hbond A_W1 solventdonor :WAT solventacceptor :WAT acceptormask :WAT|A.O
> donormask :WAT angle 135.0 dist 3.5 nointramol bridgeout watbridge1.dat
>
> This should track all bridges, like A-W-A, A-W-W and W-W-W. But it still
> doesn't.
>
> On Thu, Jun 25, 2015 at 1:20 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
> > Hi,
> >
> > On Wed, Jun 24, 2015 at 7:52 AM, DEBOSTUTI GHOSHDASTIDAR <
> > debostutighosh.gmail.com> wrote:
> >
> > >
> > > hbond A_W solventdonor :WAT solventacceptor :WAT :A angle 135.0 dist
> 3.5
> > > nointramol bridgeout watbridge.dat
> > >
> >
> > Note that you've got your ions and water in two separate masks - seems
> like
> > you want something like ':WAT,A'. Maybe this is the source of your error?
> >
> > -Dan
> >
> >
> > > hbond A_W1 solventdonor :WAT solventacceptor :WAT acceptormask :A,:WAT
> > > donormask :WAT angle 135.0 dist 3.5 nointramol bridgeout watbridge1.dat
> > >
> > > hbond W_W solventdonor :WAT solventacceptor :WAT acceptormask :WAT
> > > donormask :WAT angle 135.0 dist 3.5 nointramol bridgeout watbridge2.dat
> > >
> > > run
> > >
> > > writedata A_W_bridge.dat A_W[Bridge]
> > > writedata A_W_bridge1.dat A_W1[Bridge]
> > > writedata W_W_bridge.dat W_W[Bridge]
> > >
> > >
> > > I presumed that A_W_bridge1.dat will have information about A-W-W as
> > well
> > > as A-W-A (since both A and WAT are mentioned in the solute mask) and
> will
> > > actually be a sum of the information in A_W_bridge.dat (has only A in
> the
> > > solute mask) and W_W_bridge.dat (has only WAT in the solute mask.
> > >
> >
> > > However, this doesn't seem to be the case. The W_W_bridge.dat has far
> > more
> > > number of W-W-W bridges recorded than A_W_bridge1.dat.
> > >
> > > Where am I going wrong?
> > >
> > > Thanks in advance for any suggestions
> > >
> > > --
> > > Debostuti
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > -------------------------
> > 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)
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Debostuti
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
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 Thu Jun 25 2015 - 08:00:04 PDT
