[gmx-users] PROTEIN FOLDING

[Neha Gupta]

Thank you Joao and Aman.

I have noted the points you have suggested.

Do you think analyzing DSSP would help?

Thanks,
Neha

On Wed, Dec 20, 2017 at 4:03 PM, João Henriques <
joao.m.a.henriques at gmail.com> wrote:

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