[gmx-users] PROTEIN FOLDING

[Lakshman Ji Verma]

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
> > > > > > > > > > --
> > > > > > > > > > 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.
> > > >
> > > --
> > > 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.