AMBER Archive (2004)

Subject: Re: AMBER: minimization output

From: L Jin (s0344557_at_sms.ed.ac.uk)
Date: Fri Feb 13 2004 - 03:49:52 CST

Thank you for reply. I changed the DIELC value from 1 (default) to 4 then the
failiar vanished for most molecule minimization running. But there are still the
same problem with few others. I am curious how this DIELC affects the running.
Maybe I need to change some basic parameters instead of only this DIELC value.
Thanks.

Lan

Quoting "David A. Case" <case_at_scripps.edu>:

> On Tue, Feb 10, 2004, L Jin wrote:
> >
> > I got the top and crd file from xleap after running antechamber as before.
> > Everything seems fine. But when I ran the following command:
> >
> > 'sander -O -i min.in -o min.out -p GlcNS.top -c GlcNS.crd -r min.restrt',
> >
> > I did not get the min.restrt output file and the min.out contained the
> following
> > message which I never meet before with the same running.
> >
> > Frac coord min, max: -0.144743351 1.10900132
> > The system has extended beyond
> > the extent of the virtual box.
> > Restarting sander will recalculate
> > a new virtual box with 30 Angstroms
> > extra on each side, if there is a
> > restart file for this configuration.
> > EWALD BOMB in subroutine Routine: map_coords (ew_force.f)
> > Atom out of bounds. If a restart has been written,
> > restarting should resolve the error
> >
>
> You need to run a short minimization, printing the output every step
> (ntpr=1).
> Somehow, your system is moving by more than 30 Ang upon minimization, which
> generally does not happen. Look at the structure at the beginning, and
> after
> 10 steps or so, to see which (if any) atoms have moved a long way. You
> should
> also take note of how many steps of minimization you run before seeing the
> above message.
>
> ...good luck...dac
>
> --
>
> ==================================================================
> David A. Case | e-mail: case_at_scripps.edu
> 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 | http://www.scripps.edu/case
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