[gmx-users] Ramachandran plot

Mark Abraham mark.j.abraham at gmail.com
Wed Jun 7 10:55:42 CEST 2017


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*
> > > --
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> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
> Gromacs Users mailing list
>
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> posting!
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