Dear Anna,
Thank you for your message. But what is SYSBYL and how did you this? Removing
the clashed conform would not affect your whole running? Thanks
Regards,
Lan
Quoting Anna Schrey <anna_amber.web.de>:
> Dear Jin,
>
> I recently had the same problem - this vanished after I removed a
> sterical clash in the protein by minimizing the PRotein in SYSBYL using
> an aggregate containing all but one of the clashed residues.
>
> best regards,
>
> Anna
>
> L Jin wrote:
> >
> > Dear all,
> >
> > 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
> >
> >
> >
> > It seems that something wrong with the box. But actually I did not add any
> box
> > for my molecule. I checked the top file it is nearly the same as the one
> running
> > minimizaiton well before. Please anybody can give me some suggestion?
> Thanks in
> > advance.
> >
> > Lan
> >
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>
> --
> Dr. Anna K. Schrey
> Forschungsinstitut fuer Molekulare Pharmakologie Phone: +49-30-94793-231
> Robert-Roessle-Strasse 10 Fax: +49-30-94793-169
> D-13125 Berlin, Germany email:
> schrey.fmp-berlin.de
>
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Received on Fri Feb 20 2004 - 10:53:01 PST
