Hi Daniel
Thanks for your response. I wanted to calculate water that bridges between
two ions. 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
> > _______________________________________________
> > 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Debostuti
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Received on Thu Jun 25 2015 - 00:00:02 PDT
