Correction
On Wed, Apr 6, 2011 at 10:21 AM, Jason Swails <jason.swails.gmail.com>wrote:
> Molecular dynamics has no concept of "ligand" or "receptor". Particles are
> either there or they are not.
>
or (for TI/FEP), somewhere in between :)
>
> The only time you have to decide whether to include something as a "ligand"
> or a "receptor" is for MM/PBSA analysis. In that case, think carefully
> about what you're actually trying to measure -- that will decide where they
> should be included.
>
> Hope this helps,
> Jason
>
> On Wed, Apr 6, 2011 at 8:46 AM, sonam bhatia <sonamniper.bhatia.gmail.com>wrote:
>
>> I want to perform MD simulation on the protein containing Mg and Zn ions
>> and
>> 5 water molecules in active site which are necessary to kept during
>> simulation. I am facing problem how to consider those water molecules,
>> either part of protein or as a part of ligand?
>> Or any other method is there for their treatment?
>>
>>
>> --
>> *Sonam Bhatia,*
>> *Ph.D. Scholar,
>> Department of Medicinal chemistry,
>> National Institute of Pharmaceutical Education and Research (NIPER),
>> Sector 67, phase 10,S.A.S Nagar,
>> Punjab-160062. India*
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Apr 06 2011 - 10:30:06 PDT
