Re: [AMBER] cpptraj align using the same numbering

From: David A Case <>
Date: Wed, 16 Jun 2021 08:55:05 -0400

On Wed, Jun 16, 2021, Martin Rosellen wrote:
>I run a simulation of a hexamer and want to calculate RMSD values of
>hairpins found in each monomer. For that I want to align the protein
>body. When I aligned the first two frames in Chimera,

You don't say what command you used to do the alignment in Chimera, or, for
that matter, what commands you using in cpptraj. The latter would not place
monomer 3 on top of monomer 1 unless you had some specific arguments that
requested that.

It seems to me that you could answer your own question about what cpptraj is
doing just by visualizing the result, or by looking at the hairpin RMS
values, etc.

[Aside-- Dan, the description of the 'align' command in the manual is
circular: it just says that the 'align' command "aligns the structure". What
is the difference between this and 'rms'?]


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Received on Wed Jun 16 2021 - 06:00:05 PDT
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