Re: [AMBER] Calculating RMSF

From: Daniel Roe <>
Date: Thu, 5 Sep 2019 11:34:52 -0400


On Thu, Sep 5, 2019 at 11:20 AM Martín Pettinati
<> wrote:
> The problem is that RMSF is performed using first frame, i've checked this by changing trayectory first frame. And changing ligand position in the reference structure doesn't change the result.

The atomicfluct command measures fluctuations over all input frames,
so it is doing what it is supposed to do. Are you sure you don't want
to calculate the RMSD of the ligand to the reference? (It's not clear
to me how calculating fluctuations over 1 frame is helpful.)

Assuming RMSD is indeed what you want, just do something like:

reference crystal.crd [REF] parm crystal.prmtop
rmsd RMSD :1-578.CA,C,N,O ref [REF]
rmsd Ligand :ligand nofit out ligrmsd.dat

The 'nofit' keyword will ensure your previous alignment of the protein
to the reference is not altered. Hope this helps,


> Thank you
> Martín
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Received on Thu Sep 05 2019 - 09:00:02 PDT
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