From: Matthieu Chavent (
Date: Fri May 30 2008 - 04:12:31 CDT

Hello All,

 I have a problem: I created a water box around a protein complex to
perform MD simulations. During the MD a protein moved out the water box
and was placed at the opposite side of the water box (thank to periodic
conditions). I would like to save the trajectory in a pdb file, but when
I use save coordinates the positions of the two proteins are saved at
each side of the water box and I can't analyze the results (calculate
RMSD, residues in contact, etc..). I think that It is possible to move
one of the two protein to reconstruct the complex.. But I don't know how..

 Could you help me please...

    Thank you in advance!

     Matthieu Chavent (PhD student)