Hi,
Sorry for the delay in getting back to you.
Why not just use 'multidihedral' to calculate your dihedral values,
and then the 'avg' analysis command to calculate average/standard
deviation, the latter of which essentially gives you the dihedral
fluctuation (similar to coordinate RMS fluctuation)?
E.g.
parm myparm.prmtop
trajin mytrajectory.dcd
multidihedral PhiPsi phi psi
run
runanalysis avg PhiPsi[*] out phipsifluct.dat name Fluct
Hope this helps,
-Dan
On Fri, Jun 14, 2019 at 12:59 PM Lod King <lodking407.gmail.com> wrote:
>
> Hi Amber
>
> I ran the following command:
> > >parm myparm.prmtop
> > >trajin mytrajectory.dcd
> > >rms first
> > >average crdset MyAvg
> > >run
> > >rms ref MyAvg
> > >atomicfluct out backbone-atoms.agr .C,CA,N by byres
>
> This should give me the phi/psi angle instead of CA RMSF right?
>
> I then performed
>
> >>atomicfluct out RMSF.dat :1-198.CA byres
>
> This will give the CA rmsf only, right?
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Received on Thu Jun 20 2019 - 06:00:02 PDT
