On Wed, Jun 26, 2019 at 9:46 PM Lod King <lodking407.gmail.com> wrote:
> Thanks for the email. I got the data, but it does not give the analysis I
> wish. As I want to plot the RMSF of the system using phi/psi angle instead
> of alpha carbon.
>
> Unless I am not clear fully clear about the output data set showing below,
> it does not look right as I usually see the RMSF plot in papers with
> angstrom in the Y axis. This data set does not give me any value in A to
> plot.
OK - so if what you want is the RMSF of the angles, you want to plot
the 'Fluct[sd]' column, which contains the standard deviation of the
angles you calculated (which is equivalent to the fluctuation as
calculated for XYZ coords by 'atomicfluct'). Since you're calculating
angles, everything is in degrees - I can't envision a scenario where
you would want to report angles in Angstroms.
Hope this helps,
-Dan
>
> If someone can help me to understand, it would be really appreciated.
>
> #Set Fluct[avg] Fluct[sd] Fluct[ymin] Fluct[ymax] Fluct[yminidx]
> Fluct[ymaxidx] Fluct[names]
> 1 147.1 43.7 -179.9 180 5735
> 756 "psi:1"
> 2 -81.99 50.37 -179.8 179.9 445
> 7496 "phi:2"
> 3 132.7 42.73 -180 180 6554
> 7683 "psi:2"
> 4 -107.1 42.02 -179.7 179 2944
> 6084 "phi:3"
> 5 127.9 45.14 -179.6 180 4140
> 1055 "psi:3"
> 6 -86.8 63.01 -173.2 134.3 1572
> 1600 "phi:4"
> 7 104.6 37.88 -174.3 179.9 322
> 1708 "psi:4"
> 8 -105.8 25.88 -178.8 179.2 492
> 477 "phi:5"
> 9 123.9 44.63 -179.9 179.9 8020
> 8899 "psi:5"
> 10 -111.3 37.05 -179.9 179.7 2270
> 3680 "phi:6"
> 11 140.4 30.75 -179.9 180 2967
> 2979 "psi:6"
> 12 -95.48 23.84 -179.2 176.5 1318
> 1142 "phi:7"
> 13 111.8 20.78 -179.9 179.9 34
> 890 "psi:7"
> 14 -95.34 19.92 -178.4 179.2 9167
> 5842 "phi:8"
> 15 -3.25 31.01 -179.9 180 9806
> 9818 "psi:8"
> 16 86.23 26.53 -172.8 176.4 5817
> 5965 "phi:9"
> 17 -6.295 33.7 -179.9 180 9172
> 5807 "psi:9"
> 18 -119.1 25.13 -179.8 179.9 6275
> 5718 "phi:10"
> 19 -33.07 57.55 -180 179.9 1343
> 1177 "psi:10"
> 20 -129.9 37.52 -179.8 180 9119
> 3524 "phi:11"
> 21 150.6 54.08 -180 180 6589
> 4121 "psi:11"
> 22 -104.8 24.89 -179.8 180 1042
> 1646 "phi:12"
> 23 122.3 56.03 -179.9 180 1711
> 2491 "psi:12"
>
> On Thu, Jun 20, 2019 at 5:41 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> > 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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> >
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> >
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Received on Thu Jun 27 2019 - 08:30:07 PDT
