Hi, Sangita Kachlap
Yes, I think ASMD could be one way to compute the PMF, you can try the
first
two or three segments to see if it works well.
for me umbrella sampling or ABMD could be other possible options.
Best
Feng Pan
On Tue, Aug 21, 2018 at 6:38 AM sangita kachhap <nckachap.cyf-kr.edu.pl>
wrote:
> Dear All,
> I have a metalloprotein (dimer) with docked ligand in the binding site of
> one of the monomer. ligand is approx at a distance of 9 angstrom from the
> catalytic site of same monomer. Movement of ligand towards the catalytic
> site will trigger protein to get close conformation and enzyme catalysis
> will take place.
> I did classical MD simulation of docked complex but during simulation
> ligand is moving out from the binding site.
> Will ASMD be appropriate here to calculate PMF for bringing ligand to
> active site at a distance of 2-3 angstrom? Or any other method I can do?
>
> Thanks
>
> ----------------------------------------------
> Sangita Kachhap
> Post Doctoral FellowJerzy Haber Institute of Catalysis and Surface
> Chemistry
> Polish Academy of Sciences
> Niezapominajek 8
> PL-30239 Krakow, Poland
>
> ----------------------------------------------
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Feng Pan
Ph.D.
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 21 2018 - 21:00:02 PDT
