[AMBER] cpptraj: rmsd problem

From: Thomas Fox <thomas_fox.gmx.net>
Date: Tue, 7 Jul 2015 11:15:34 +0200


   I may be stupid, but Im struggling with the results of the rmsd command in

   Scenario1: protein without water (170 residues)
   I take the original structure, and the same structure where all
   x-Coordinates are shifted by 1 A.
   I save the two structures as pdb files and load them into cpptraj
   Then I issue
   rmsd first out x0

   As expected, the calculated rmsd is 0. for both frames

   Scenario2: same protein with water box (truncated octahedral box, ~6700
   same procedure, all x-coordinates shifted by 1 A for the second frame.

   rmsd first out x0

   gives in x0:
   #Frame RMSD_00000
   1 0.0000
   2 1.2029

   This is something that I do not understand: I would expected the same result
   as in scenario 1.

   Interestingly, if I do a "strip :WAT" first, the RMSD for the second frame
   increases to 1.5; the size of the shift has no effect on the calculated

   Whas is going on here? Is this a numerical problem of the RMSD routine for a
   large number of atoms ? Some weird effect of a truncated-octahedral box
   (doubt it, because using the original pdb as parm, i.e. no box info present
   at all, produces the same results? Or a general misconception from my side
   how the rmsd command should work?

   Thanks a lot,

   PS. I use Amber14, cpptraj V14.01
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Received on Tue Jul 07 2015 - 02:30:03 PDT
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