Hi Dan
Thats right....and that works fine where I get *only* A-W-A bridges. But I
also want A-W-W bridges...in that case I should mention both WAT and A as
solute right?
Thanks
On Thu, Jun 25, 2015 at 8:18 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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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> > > >
> > >
> > >
> > >
> > > --
> > > -------------------------
> > > 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)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Debostuti Ghosh Dastidar
PhD Scholar
Computational Biophysics Lab
Department of Biotechnology
Indian Institute of Technology Madras
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Received on Thu Jun 25 2015 - 22:00:03 PDT
