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
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.
Any reply would be appreciated. Thanks.
Lan
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Received on Mon Feb 16 2004 - 14:53:01 PST
