[gmx-users] PROTEIN FOLDING

[RAHUL SURESH]

Also you must know, a lot analysis are available over the entire manual of
Gromacs where all cannot be performed. Gromacs always provide you all
necessary analysis but to choose which one is always your choice that suits
your simulation purpose.


On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta <nehaphysics17 at gmail.com> wrote:

> 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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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*