AMBER Archive (2003)

Subject: Re: job stopped

From: Natasja Brooijmans (nbrooij_at_itsa.ucsf.edu)
Date: Thu Apr 24 2003 - 13:55:06 CDT

You would still have to visualize the starting and final coordinates in
some graphics program to see what happened. Perhaps your ligand is not
bound any more.

Natasja Brooijmans, Ph.D.
Visiting Post-Doctoral Scholar
Kuntz Laboratory
Department of Pharmaceutical Chemistry
University of California, San Francisco
San Francisco, CA 94143-2240
phone: 415-476 3986
fax: 415-502 1411
e-mail: nbrooij_at_itsa.ucsf.edu

On Thu, 24 Apr 2003, Youyi Peng wrote:

> Thanks.
> But there is no solvent molecules included in my system. I ran vacuum MD on
> unconstrainted ligand-protein complex.
> ---Youyi
>
> "CUI, Guanglei" wrote:
>
> > Hi,
> > I've come across this problem a few times as well. In my case, it was
> > because some unrestrained water molecule estrayed into the vacuum. Do
> > you have solvent molecules included in your system? You can check
> > your final restart file or MD snapshot and see if this's the case.
> >
> > cuigl
> >
> > On Thu, 24 Apr 2003, Youyi Peng wrote:
> >
> > > Hi,
> > > I ran a 1 ns MD on a vacuum system in a Linux Bash shell. After 220 ps,
> > > the job was stopped and
> > > I found the following error message at the end of output file. I don't
> > > understand what happened.
> > > Please help me.
> > >
> > >
> > > "Frac coord min, max: -0.000107843448 0.737832413
> > > 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"
> > >
> > > Thank you very very much!
> > >
> > > ----Youyi
> > >
> > >
> >
> > --
> > Guanglei Cui
> > Dept. of Chemistry
> > SUNY at Stony Brook
> > Stony Brook, NY 11790
>
>