Thanks Dan
I figured out that the problem is with my system. When I have only WAT in
the mask, it gives me WAT-WAT bridges. But when I give WAT and A in mask,
some of the bridged waters are also bridged with A, hence those bridges are
not given separately as WAT-WAT bridges alone.
Thanks for the help
On Sat, Jun 27, 2015 at 7:06 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Yes! I had totally forgotten about this but when you automatically search
> for donors/acceptors then solvent is excluded. This is done because in most
> cases (e.g. when no mask is specified) you are only interested in
> solute-solute and solute-solvent hydrogen bonds, not solvent-solvent. So
> you do actually need to force cpptraj to treat water as a "solute" acceptor
> and donor via 'donormask' and 'acceptormask':
>
> hbond A_W_W donormask :WAT,A acceptormask (:WAT.O)|(:A) \
> solventdonor :WAT solventacceptor :WAT.O \
> dist 3.5 angle 135.0 bridgeout watbridge2.dat
>
> Hopefully this works for you,
>
> -Dan
>
> PS - Note that the 'bridge' functionality was originally designed with just
> tracking solute-solvent-solute bridges in mind, which is why setting this
> up is not so straightforward. I am currently busy with some personal
> matters (which is why responses are sometimes slow) but I am trying to work
> on this when I can - it may be that the 'bridge' functionality needs to be
> expanded in the future...
>
>
>
> On Fri, Jun 26, 2015 at 10:45 PM, DEBOSTUTI GHOSHDASTIDAR <
> debostutighosh.gmail.com> wrote:
>
> > Hi Dan,
> >
> > I can't figure out why the above command is not working for me. From the
> > setup messages I can understand that "hbond A_W_W :WAT,A solventdonor
> :WAT
> > solventacceptor :WAT.O" is only considering A in mask. So essentially
> the
> > above command is giving me the same number of bridges as "hbond A_W_W :A
> > solventdonor :WAT solventacceptor :WAT.O", which means WAT is not
> getting
> > counted in the mask. However, if I give water separately in acceptormask
> or
> > donormask then it is getting counted, as I had mentioned in my first
> mail.
> > But unfortunately thats not giving me all the bridges.
> >
> > In fact ":WAT|A.O" shows me the right number of donors and acceptors
> > (water
> > + anion) (even the manual says that we can use logical operands in
> mask?pp
> > 486 in Amber14 manual). But even that does not give me the correct A-W-W
> > bridges:(
> >
> > Thanks for the help
> >
> > On Fri, Jun 26, 2015 at 10:55 PM, Daniel Roe <daniel.r.roe.gmail.com>
> > wrote:
> >
> > > 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
> > >
> >
> >
> >
> > --
> > 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
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Received on Mon Jun 29 2015 - 10:30:02 PDT
