ptraj to re-associate protein+DNA

From: Michael Cooney <mike_at_bmbiris.bmb.uga.edu>
Date: Wed 25 Jul 2001 17:34:29 -0400 (EDT)

Dear Amber users,

I've tried ptraj to re-associate the peptide and DNA in a complex where
they dissociated after ~900 ps of MD in a water box, but find that
unfortunately ptraj fails to bring them together after this time point.
A sample input input file is:

trajin prodmd_gata_rest5.crd.Z
trajout gata_6th_ctr.crd
center image
go

I am including all atoms, solute and solvent, in the process.

Any suggestions would be greatly appreciated. Thanks in advance.

Sincerely,

Michael G. Cooney
University of Georgia
Athens, GA 30602 USA
Received on Wed Jul 25 2001 - 14:34:29 PDT