[gmx-users] Ramachandran plot

[RAHUL SURESH]

Thank you Dear Mark.

Its my pleasure taking your time. ;-)

On Wed, Jun 7, 2017 at 2:25 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> This is why you should actually copy and paste your command lines so you
> don't waste your time ;-) And mine.
>
> Unless you wrote your entire system to your xtc file, your tpr has more
> atoms than your xtc, and thus probably some more dihedrals. Make a matching
> subset of your tpr using gmx convert-tpr, and use that with gmx rama -s.
>
> Mark
>
> On Wed, Jun 7, 2017 at 10:41 AM RAHUL SURESH <drrahulsuresh at gmail.com>
> wrote:
>
> > Dear Mark
> > Thank you
> >
> > gmx rama -f traj.xtc -s topol.tpr -o ramachandran.xvg
> >
> > This was my command..
> >
> > I didn't choose any dihedral particularly
> >
> >
> > On Wed, 7 Jun 2017 at 2:00 PM, Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > Sounds like your choice of dihedrals doesn't match your system. How did
> > you
> > > select them?
> > >
> > > Mark
> > >
> > > On Wed, 7 Jun 2017 08:41 RAHUL SURESH <drrahulsuresh at gmail.com> wrote:
> > >
> > > > Dear Users
> > > >
> > > > When I try to execute ramachandran plot analysis, I get the following
> > > note
> > > > like "Dihedral around 5809,5816 not found in topology. Using mult=3"
> > > > (nearly 30-40 dihedrals). What is it about?
> > > >
> > > > Input is just protein structure extended upto 150ns.
> > > >
> > > > --
> > > > *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.
>



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