Molecular dynamics has no concept of "ligand" or "receptor". Particles are
either there or they are not.
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 06 2011 - 10:30:05 PDT
