But I am doing the same thing first adding ions then solvating the system.
> 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
>>>>
>>>>
>>>> _______________________________________________
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>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>>
>>>
>>> --
>>> Dmitry Nilov,
>>> Faculty of Bioengineering and Bioinformatics,
>>> Lomonosov Moscow State University
>>>
>>> _______________________________________________
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>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>> Sangita Kachhap
>> JRF
>> BIC,IMTECH
>> CHANDIGARH
>>
>>
>> _______________________________________________
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>>
>
>
>
> --
> Dmitry Nilov,
> Faculty of Bioengineering and Bioinformatics,
> Lomonosov Moscow State University
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Wed Mar 30 2011 - 03:00:04 PDT
