Re: [AMBER] Backbone Rmsd

From: Jason Swails <>
Date: Fri, 20 Mar 2015 21:26:32 -0400

On Fri, Mar 20, 2015 at 6:03 AM, jacob wick <> wrote:

> Thanks David,
> I worked on the two systems. But the latter one didn't work.
> Can you please suggest what is the reason.
> rms first out rna_run.rms @P,O3',O5',C3',C4',C5' time 0.50
> rms first out rna_test.rms @!P,O3',O5',C3',C4',C5' time 0.50 nofit

​What is the second mask supposed to select? Because it probably isn't
selecting what you think it is.

You can use the "mask" command in cpptraj to print out the atoms selected
by a mask to verify it selects what you intend.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Fri Mar 20 2015 - 18:30:02 PDT
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