However during the setup it shows the correct number of acceptors, donors,
solvent acceptors and solvent donors.
On Thu, Jun 25, 2015 at 12:05 PM, DEBOSTUTI GHOSHDASTIDAR <
debostutighosh.gmail.com> wrote:
> Hi Daniel
>
> Thanks for your response. I wanted to calculate water that bridges between
> two ions. 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
>
--
Debostuti
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Received on Thu Jun 25 2015 - 00:00:03 PDT
