AMBER Archive (2003)

Subject: Re: job stopped

From: CUI, Guanglei (cuigl_at_morita.chem.sunysb.edu)
Date: Thu Apr 24 2003 - 15:32:29 CDT

Could you turn on CPK rendering or sphere rendering because if something
really small is leaving your system, you might not notice it with line
drawing model?

On Thu, 24 Apr 2003, Youyi Peng wrote:

> I checked the structures of the starting conformation and the restart
> file. The ligand doesn't fly away and stays the position very similar to
> the starting one. The binding site for the ligand is interhelical. It is
> not easy to go too far.
> ---Youyi
> Yong Duan wrote:
>
> > Could the ligand fly away? Just a guess ...
> >
> > yong
> >
> > -----Original Message-----
> > From: yypeng_at_UMDNJ.EDU [mailto:yypeng_at_UMDNJ.EDU] On Behalf Of Youyi Peng
> > Sent: Thursday, April 24, 2003 2:50 PM
> > To: CUI, Guanglei; amber_at_heimdal.compchem.ucsf.edu
> > Subject: Re: job stopped
> >
> > 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
>
> 

-- 
Guanglei Cui
Dept. of Chemistry
SUNY at Stony Brook
Stony Brook, NY 11790