AMBER Archive (2001)

Subject: dissociation of protein from DNA in MD

From: Michael Cooney (mike_at_bmbiris.bmb.uga.edu)
Date: Sat Jul 21 2001 - 14:50:27 CDT

Dear Amber users,

I have started using iwrap=1 in simulations of solvated protein:DNA
complexes, as has been suggested to keep all atoms in the same box image.
However, after ~800 ps the DNA (16bp) still appears to dissociate from the
peptide (66 aa). Is ptraj still needed to bring these noncovalently bonded
components back into the same box?

Thanks for your help.

Sincerely,

Michael G. Cooney
Dept. of Biochemistry and Molecular Biology
The University of Georgia
Athens, GA 30602, USA