[gmx-users] ED of protein-DNA complex

ravishk kumar kumar.ravishk at gmail.com
Sat Aug 4 17:57:01 CEST 2007

Dear gmx-users,
I am trying to extract the ED of a trajectory of protein-DNA complex.
I have done the simulation in AMBER and renamed the trajectory to .g87
i extracted out a PDB from first frame of the trajectory and use this as
toplogy file.

Diagonalising the eigen vector:

g_covar -f nowat.g87 -s evxone.pdb -fit -v eigen  -o eigenval
I selected the gromos g87 format with box info.
least square fit i done with protein and diagonalised with C-alpha atoms

 g_anaeig -v eigen.trr -s evxone.pdb -f nowat.g87 -proj proj.xvg -comp
comp.xvg -last 10

The output i get is huge value against each of eigen vector.

I viewed this projection in IED, it shows movement of the whole molecule
along one plane in both negative and positive axis, in which the topology
file (PDB) is at centre and the trajectory on eigen vector move away from
But if i take a sample output from website (IED itself), it shows motion in
a restricted manner(only the backbone is moving and not the positional
displacement of whole molecule ).

why it is so?. i thought my molecule is moving inside the box while
simulation, hence i fit all the trajectory frames to the initial frame, but
the same trend is seen.
my projection values were:
 0.0000  -15.78773
   10.0000  -24.27282
   20.0000  -27.06960
   30.0000  -26.87637
   40.0000  -25.94341
   50.0000  -20.00264
   60.0000  -18.31344
   70.0000   -9.77106
   80.0000   -7.00634
   90.0000   -3.74432
  100.0000   -6.99674
  110.0000   -4.79401
  120.0000  -12.33676
  130.0000   -5.88940
  140.0000   -8.95927
  150.0000  -14.07851
  ..............   .............
and so on.

What can be the mistake in the projection. I am seeing projection values
which were low for most simulation.

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