[AMBER] query reg ptraj RMSD calculation

From: Asmita Gupta <asmita4des.gmail.com>
Date: Thu, 12 Sep 2013 19:15:18 +0530

Dear users,

I am trying to calculate RMSD of two different RNA double helices with
respect to initial crystal structure. These 2 structures differ by a single
base-pair substitution from X-ray strc.

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 different..so
hw superposition and rms calculation is done?

And this rms involves fitting of all heavy atoms. so it is not like as if i
am fitting with respect to backbone only...the base heavy atoms are also
involved..though i am getting some values..but a bit confused about the


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Received on Thu Sep 12 2013 - 07:00:03 PDT
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