[gmx-users] PROTEIN FOLDING

[João Henriques]

"You can use various supporting tools from R language to debug your
trajectory but most third party software support NAMD and charmm format.
You can use VMD to convert the trajectory to dcd and use R language based
packages to read your trajectory"

What? How is this useful or helpful? At most it confuses the OP even more.

Also, the clustering analysis is unlikely to be what you want or need at
this stage. Why overcomplicate? One of the simplest ways to check that
there are conformational changes on a given set of atoms is by doing a RMSD
analysis using the folded structure as the reference. The RMSD is somewhat
degenerate, but should suffice for this purpose. You can use an index file
to restrict the RMSD analysis to a particular subset of your system (the
docking site, for example).

You could look at the radius of gyration as well, Rg, as Aman Deep also
suggests. This can either be calculated on a subset of atoms or on the
entire protein. The latter could potentially be used to compare with the
experimental reference obtained by SAXS, for example. Or you could
calculate the SAXS curve and get a better understanding of size and shape
differences between your protein and the reference, but that's more
advanced stuff.

J

On Tue, Dec 19, 2017 at 9:52 AM, RAHUL SURESH <drrahulsuresh at gmail.com>
wrote:

> 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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> > > *Rahul Suresh*
> > > *Research Scholar*
> > > *Bharathiar University*
> > > *Coimbatore*
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> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
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