Indeed, some crystal waters as well as additional waters can be
replaced by ions.
I just suppose you can run "addions" prior to "solvatebox" (I have
never done this by myself). In this way you will be shure that you
have N-M crystal waters where M - the number of added ions.
On Wed, Mar 30, 2011 at 12:45 PM, Sangita Kachhap <sangita.imtech.res.in> wrote:
>
> 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
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>>
>> --
>> Dmitry Nilov,
>> Faculty of Bioengineering and Bioinformatics,
>> Lomonosov Moscow State University
>>
>> _______________________________________________
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>>
>
>
> Sangita Kachhap
> JRF
> BIC,IMTECH
> CHANDIGARH
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dmitry Nilov,
Faculty of Bioengineering and Bioinformatics,
Lomonosov Moscow State University
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Received on Wed Mar 30 2011 - 02:30:02 PDT
