In PDB crystal water molecules are from 161 to 388 after protein - DNA complex.
In tleap I have add Na+ to it now numbring of crystal water has been changed.
First DNA, protein, Na+ then finaly WAT (including both crystal and TIP3P water)
How here I can define the N crystal waters?
> Hello!
> Note, that TIP3P is just a water model by which both ctystal waters
> and additionally added waters will be treated during MD simulation.
> I believe that additional waters are added by solvatebox command after
> N crystal waters in input PDB. Thus you can just apply ambermask to N
> residues following protein-DNA residues.
>
> On Wed, Mar 30, 2011 at 11:30 AM, Sangita Kachhap <sangita.imtech.res.in> wrote:
>>
>> Hello all
>>
>> I have a protein-DNA complex and I have to add crystal water in MD simulation
>> of
>> solvater protein-DNA complex with crystal water as well as well I have to use
>> positional restraint on crystal water.
>>
>> So here how I discriminate between crystal water and TIP3P water for applying
>> positional
>> restraint?
>>
>>
>> Sangita Kachhap
>> JRF
>> BIC,IMTECH
>> CHANDIGARH
>>
>>
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>
>
>
> --
> Dmitry Nilov,
> Faculty of Bioengineering and Bioinformatics,
> Lomonosov Moscow State University
>
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>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Wed Mar 30 2011 - 02:00:04 PDT
