Hi John,
It looks good to me. I have calculated atomic fluctuations in a similar
manner after having created an average structure from my trajectory as a
reference. However, in order to remove the translational motion, I aligned
to a different selection (one that gives me the best fit) than for which I
calculated the fluctuations.
trajin ../../../../traj/chA_e20ps_100ns.mdcrd 1 5000 2
reference ../refs/chA_avestruct.pdb
rms reference ":4-56.CA"
atomicfluct out atomicfluct/chA_atomicfluctCA.out ":1-66.CA" byres
Hope this helps.
Sincerely,
Logan
On Sat, Dec 11, 2010 at 11:36 PM, John S <s.john634.gmail.com> wrote:
> Dear Amber Users,
>
> I am using atomicfluct to calculate the rmsf , I presume the units are in
> Angstrom .
>
> Is is related to translational motion only .
> I used it as below
>
> trajin md.x
> reference ../all.pdb
> rms reference out rms :1-12.S1,C2,C3,C4,C5
>
> atomicfluct out file.dat :1-12.S1,C2,C3,C4,C5 byres
>
> Can anyone suggest , on the way I have specified the reference structure
> from where it will calculate the fluctuations (i.e an average structure),
> is
> correct or not .I appreciate your help.
>
> Thanks
> John
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Received on Sun Dec 12 2010 - 06:30:05 PST
