AMBER Archive (2002)

Subject: ptraj rmsd calculation

From: Thomas Steinbrecher (thomas.steinbrecher_at_physchem.uni-freiburg.de)
Date: Thu Dec 05 2002 - 14:15:40 CST

Dear AMBER users,

I used ptraj to calculate the rmsd values of protein
snapshots from an MD trajectory comparing them to the
starting structure. My ptraj-command is:

------
ptraj complex.prmtop << EOF
trajin complex_equi3.crd
image
strip :WAT
center
rms first out complex_equi3.crd.rmsd @CA,C,N
EOF
------

This results in these values for the 20 frames,
corresponding to a total of 200 ps of simulation:

    1.00 0.00000 2.00 0.86810
    3.00 0.94004 4.00 0.97595
    5.00 0.92930 6.00 0.87957
    7.00 0.90640 8.00 0.93602
    9.00 0.90414 10.00 0.83537
   11.00 0.88181 12.00 0.88361
   13.00 13.01500 14.00 1.10511
   15.00 13.04624 16.00 12.96831
   17.00 12.94386 18.00 12.98768
   19.00 13.00800 20.00 12.96959

I wonder why the values are so large for frame 13 and
15-20. The trajectory looks quite "normal" when viewed with
vmd (no change in the protein's overall shape can be seen)
and if I rerun ptraj and calculate the rmsd for only 1
residue, all the rmsd-values lie below 1.5 A.

When I make pdb-files from my frames and compare them to
the first one, all rmsd-values are <1.5 A.

Is it possible that something is wrong with my ptraj input?
Has anyone experienced similar results with the ptraj rms
command?

Kind regards,

Thomas