Hi,
I may be stupid, but Im struggling with the results of the rmsd command in
ptraj.
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
waters)
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
rmsd.
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,
Th.
PS. I use Amber14, cpptraj V14.01
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Received on Tue Jul 07 2015 - 02:30:03 PDT
