AMBER Archive (2004)

Subject: Re: AMBER: minimizating complex-protein with AMBER

From: David A. Case (
Date: Sun Feb 15 2004 - 23:14:02 CST

On Sun, Feb 15, 2004, wrote:
> I am using Amber 7 to minimize complex-structure constituted by three
> chains (370 Amino acids).
> The minimization stops after nstep = 10 and in the file nome.min.out ais
> indicated this error:
> The system has extended beyond
> the extent of the virtual box.

There is almost certainly something very wrong with your starting
configuration. In only 10 steps of minimization, some atoms have moved
more than 30 Ang. You should look carefully at the structure and at the
initial energies to try to find bad contacts. The "checkoverlap" command
in ptraj is often very useful in finding problems with your initial



================================================================== David A. Case | e-mail: Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to