Re: [AMBER] Problem related to the trajectory analysis

From: Jason Swails <>
Date: Wed, 3 Oct 2012 21:38:23 -0400

On Wed, Oct 3, 2012 at 2:20 PM, Sindrila Dutta banik <> wrote:

> Dear all
> I want to analyze the rmsd of the backbone of a protein structure. The
> protein is dimer and residue 1-396 and 398-793 are the amino acids. The 397
> and 794 no residue are the substrates for two chain. I have the trajectory
> file. I use the following to compute the rmsd in the script file
> rms first out BB.out :1-396.CA,N,C :398-793.CA,N,C time 0.1
> Is it correct? Is it compute the rmsd of backbone for two chains?

No. The RMSD command takes one mask. So do this:

rms first out BB.out :1-396,398-793.CA,N,C time 0.1

Also, for 2 chains there is a possibility of imaging artifacts caused by
wrapping. If you visualize the system and one chain appears to 'jump' to
the other side of the solvent box, you should reimage (perhaps using the
'autoimage' command in cpptraj) before performing the RMS command.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Wed Oct 03 2012 - 19:00:03 PDT
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