On Thu, Jun 25, 2015 at 10:48 PM, DEBOSTUTI GHOSHDASTIDAR <
debostutighosh.gmail.com> wrote:
> 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?
>
Yes, except the mask you used before (:WAT|A.O) isn't valid - I'm surprised
you don't get an Error or Warning message. The 'A' in the mask as stated
isn't described as a residue or an atom. Instead, you want:
hbond A_W_W :WAT,A solventdonor :WAT solventacceptor :WAT.O \
dist 3.5 angle 135.0 bridgeout watbridge2.dat
Hope this helps,
-Dan
>
> 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
> > > > > _______________________________________________
> > > > > 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
> > > _______________________________________________
> > > 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
> _______________________________________________
> 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
Received on Fri Jun 26 2015 - 10:30:03 PDT
