Re: [AMBER] backbone rmsd between mutant trajectories, comparing conformational space sampled

From: David A Case <>
Date: Mon, 11 Jan 2021 08:18:40 -0500

On Mon, Jan 11, 2021, Vaibhav Dixit wrote:

>I have simulated two protein structures in which only one residue was
>mutated and thus backbone sequence is the same.
>I'm guessing it must be possible to use cpptraj to align the backbone
>coordinates frame-by-frame, and estimate rmsd to check if the mutants
>sample the same conformational space.
>parm prot-top
>reference prot.inpcrd
>trajin parm

The command you want is "rms", something like this:

rms reference :1-141.C,CA,N out rms.dat

The manual shows lots of keywords that can be added to the rms command, but
this should get you going.


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Received on Mon Jan 11 2021 - 05:30:05 PST
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