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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Received on Wed Mar 30 2011 - 01:30:02 PDT
