Hi, Dan
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.
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?
> > _______________________________________________
> > 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
>
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Received on Wed Jun 26 2019 - 19:00:04 PDT
