AMBER Archive (2001)

Subject: ptraj to re-associate protein+DNA

From: Michael Cooney (mike_at_bmbiris.bmb.uga.edu)
Date: Wed Jul 25 2001 - 16:34:29 CDT

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