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)
> > > > > _______________________________________________
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> > > > > 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)
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> > > 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
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Received on Fri Jun 26 2015 - 22:00:02 PDT
