[gmx-users] PROTEIN FOLDING

[Neha Gupta]

Hi,


Thank you for your prompt reply.

By clustering analysis, are you talking about gmx cluster command?

"over particular PC sub space"

Could you please elaborate a bit?

Thanks a lot once again.

Thanks,
Neha

On Tue, Dec 19, 2017 at 1:22 PM, RAHUL SURESH <drrahulsuresh at gmail.com>
wrote:

> On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta <nehaphysics17 at gmail.com>
> wrote:
>
> > Hi gromacs users,
> >
> > After MD simulation of protein-ligand complex for 5ns, can we view
> protein
> > folding?
> >
> > How to do it?
> >
> > I want to ascertain if there is any conformation change in protein where
> > the ligand binds. Is it possible?
> >
> > We observe hydrogen bonds through molecular docking. Hence, I want to
> make
> > observation through MD simulation which is not obtained through docking.
>
>
> You can perform Clustering analysis over particular PC sub space to measure
> the structural changes.
>
> >
> >
> > Can someone help me regarding this?
> >
> > Thank you very much in advance.
> >
> > Thanks,
> > Neha
> > --
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> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
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