Re: [AMBER] query reg ptraj RMSD calculation

From: Daniel Roe <>
Date: Thu, 12 Sep 2013 09:32:58 -0600


On Thu, Sep 12, 2013 at 7:45 AM, Asmita Gupta <> wrote:
> Now, my doubt is how does ptraj go about fitting/superposing the structures
> onto the reference, when the structures are not same...the chemical
> equivalence and the no of atoms in both the structures are
> hw superposition and rms calculation is done?

In ptraj, it is assumed that the mask you use selects the same atoms
in the target as in the reference with the same ordering.

In cpptraj you can specify both a target mask and a reference mask,
which may help in your situation. As long as you ensure that the same
# of atoms are selected with each mask the rms calculation will be

For example, say for some reason I wanted to get the RMSD between some
atoms in a methionine (target) and a lysine (reference) residue, I
could do something like:

rms reference :MET.C,CA,N,CB,CG,SD,CE :LYS.C,CA,N,CB,CG,CD,CE

The first mask is the target mask (i.e. corresponding to your input
frames), and the second mask is for the reference.

Hope this helps,


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Thu Sep 12 2013 - 09:00:03 PDT
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