Re: [AMBER] query reg ptraj RMSD calculation

From: Daniel Roe <>
Date: Thu, 12 Sep 2013 10:12:33 -0600

On Thu, Sep 12, 2013 at 9:50 AM, Asmita Gupta <> wrote:
> ok..but what if # of atoms are different?? say i have a target RNA helix
> with 841 heavy atoms, and reference helix has 844 heavy atoms (which is the
> case in my structures) is fitting done in such cases?

The definition of RMSD requires that the number of atoms in the target
and reference be the same (it doesn't make sense otherwise). What you
need to do is choose your target and reference masks such that they
select the same # of atoms. For instance in the example I gave, the
methionine residue has 16 atoms and the lysine residue has 21, yet I
chose my target and reference masks such that only 7 common atoms in
each are selected for the RMSD calculation. Note that the atoms
themselves do not need to be the same, but they should correspond
(like the CD in LYS to SD in MET).


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 - 09:30:03 PDT
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