[gmx-users] PROTEIN FOLDING

[Neha Gupta]

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
> > > > > > >
> > > > > > > * Please search the archive at
> > > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
> > before
> > > > > > > posting!
> > > > > > >
> > > > > > > * Can't post? Read http://www.gromacs.org/
> Support/Mailing_Lists
> > > > > > >
> > > > > > > * For (un)subscribe requests visit
> > > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_
> > gmx-users
> > > > or
> > > > > > > send a mail to gmx-users-request at gromacs.org.
> > > > > > >
> > > > > > --
> > > > > > *Regards,*
> > > > > > *Rahul Suresh*
> > > > > > *Research Scholar*
> > > > > > *Bharathiar University*
> > > > > > *Coimbatore*
> > > > > > --
> > > > > > Gromacs Users mailing list
> > > > > >
> > > > > > * Please search the archive at http://www.gromacs.org/
> > > > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > > > >
> > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > > >
> > > > > > * For (un)subscribe requests visit
> > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_
> gmx-users
> > > or
> > > > > > send a mail to gmx-users-request at gromacs.org.
> > > > > >
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at
> > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > > posting!
> > > > >
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-request at gromacs.org.
> > > > >
> > > > --
> > > > *Regards,*
> > > > *Rahul Suresh*
> > > > *Research Scholar*
> > > > *Bharathiar University*
> > > > *Coimbatore*
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at http://www.gromacs.org/
> > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-request at gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/
> > > Support/Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>