Thanks Feng, for the suggestion.
Regards
----------------------------------------------
Sangita Kachhap
Post Doctoral FellowJerzy Haber Institute of Catalysis and Surface Chemistry
Polish Academy of Sciences
Niezapominajek 8
PL-30239 Krakow, Poland
----------------------------------------------
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08/22/18,
12:57:26 PM
On Wed, Aug 22, 2018 at 5:35 AM Feng Pan <fpan3.ncsu.edu> wrote:
> 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
> >
> > ----------------------------------------------
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> >
>
>
> --
> Feng Pan
> Ph.D.
> North Carolina State University
> Department of Physics
> Email: fpan3.ncsu.edu
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Received on Wed Aug 22 2018 - 04:00:02 PDT
