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
Received on Sat Jun 27 2015 - 07:00:02 PDT
