Re: [AMBER] RMSF CPPTRAJ

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Thu, 20 Jun 2019 08:41:34 -0400

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?
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 20 2019 - 06:00:02 PDT
Custom Search