[gmx-users] PROTEIN FOLDING

Thu Dec 28 12:26:01 CET 2017

I gave

gmx trjconv -pbc nojump -s  prd.gro -f prd.xtc -e 50000.0 -n index.ndx -o
PRD.pdb

Is there any other alternate command?

Thanks,
Neha

On Thu, Dec 28, 2017 at 11:30 AM, RAHUL SURESH <drrahulsuresh at gmail.com>
wrote:

> Hi,
>
> migh be visualization error
>
> Apply pbc
>
> On Thu, Dec 28, 2017 at 11:06 AM, Neha Gupta <nehaphysics17 at gmail.com>
> wrote:
>
> > Hi,
> >
> > I tried running the simulations for 50 ns.
> >
> > The protein breaks (but ligand remains in the active site of the protein
> > and it is stable throughout )
> >
> > How to fix it?
> >
> > Thanks,
> > Neha
> >
> > On Wed, Dec 20, 2017 at 6:28 PM, João Henriques <
> > joao.m.a.henriques at gmail.com> wrote:
> >
> > > Depends. If you're interested in local folding and there are SS motifs
> in
> > > the region you're interested, then yes. If not, no. In terms of overall
> > > folding of the entire protein, yes it surely can be an important
> > analysis.
> > >
> > > J
> > >
> > > On Wed, Dec 20, 2017 at 1:46 PM, Neha Gupta <nehaphysics17 at gmail.com>
> > > wrote:
> > >
> > > > 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
> > > > > > > > > --
> > > > > > > > > Gromacs Users mailing list
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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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> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
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