I have one more qestion as I have to find out water mediated H-Bond betwen
protein and DNA
so I have inculde solventneighbor, solventdonor, solventacceptor in command:
hbond solventneighbor 5 solventdonor WAT O solventacceptor WAT O H1
solventacceptor WAT O H2 time 2 print .05 series hbt
It is giving interaction betwen:
solventdonor WAT O
solventacceptor WAT O H1
solventacceptor WAT O H2
and either protein or DNA
Here how I can decide that inteacting residues of protein and DNA those
interacting with water actualy interacting with
each other like in crystal structure i.e. water mediated interaction
please clear me this
> On Sat, Feb 26, 2011, case wrote:
>
>> On Sat, Feb 26, 2011, Sangita Kachhap wrote:
>> > Yes I have used mask as suggested but again getting same warning
>> >
>> > acceptor mask :1-24,26-43,45-47,48-57,59-73,75-146.N
>> > :1-24,26-43,45-47,48-57,59-73,75-146.H
>>
>> Are you really looking carefully at the prolines? The above mask suggests
>> you have prolines at residues 25,44,58 and 74 (4 total). Is that correct?
>
> Another thing to check: if residue 1 is a protonated NH3 group, then it won't
> have an atom named "H" either.
>
> ...dac
>
>
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Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Sun Feb 27 2011 - 00:00:02 PST
