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 - 09:53:00 PST
