[gmx-users] PROTEIN FOLDING

Thu Dec 28 14:33:22 CET 2017

Hi,

I tried this one

gmx trjconv -s prd.tpr -f trajwhole.xtc -pbc cluster -o trajclust.xtc -n
index.ndx

This asks me to select a group fro clustering and then select a group for
output..

What should I select first and then next?

Thanks,
Neha

On Thu, Dec 28, 2017 at 5:44 PM, Lakshman Ji Verma <lakshmanjivrm at gmail.com>
wrote:

> Do it multiple times by center the ligand first and then protein in the
> other step,while using pbc. Use -pbc mol option in one of the step to get
> the whole molecule.
>
> Thanks
>
> On Thu, Dec 28, 2017 at 6:26 AM Neha Gupta <nehaphysics17 at gmail.com>
> wrote:
>
> > 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
> > > > > > > > > > > --
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> > > > > > > > > > --
> > > > > > > > > > *Regards,*
> > > > > > > > > > *Rahul Suresh*
> > > > > > > > > > *Research Scholar*
> > > > > > > > > > *Bharathiar University*
> > > > > > > > > > *Coimbatore*
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> > > > > > > > *Research Scholar*
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> > > --
> > > *Regards,*
> > > *Rahul Suresh*
> > > *Research Scholar*
> > > *Bharathiar University*
> > > *Coimbatore*
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