Hello all,
Someone here wants to run a refinement along the lines of the old xplor
refine_gentle.inp (long rMD run, full VDW & electrostatics). Has anyone
done something like this using the python interface? Over the weekend, tried
replacing initNBond() with things like:
------
xplor.command("""
parameter
nbonds
tolerance=0.5
repel=0 cutnb=11.5 ctonnb=9.5 ctofnb=10.5 tolerance=0.5 rdie vswitch switch
end
end
""")
potList.append( XplorPot('VDW') )
#
# with or without: potList.append( XplorPot('ELEC') )
#
------
with "repel=0", VDW energies remain very high (+5000-8000) and
similarly ELEC values are ~ +1000.
not setting "repel=0" gives low, but still postive values.
Any ideas whether it's the parameter/topology set ('protein'), or REPEL being
assumed elsewhere in the python code, or -- most likely -- operator
error at this end? We can certainly just use the old-xplor refine
scripts, but would like to move to python as much as possible, so it
seemed worth asking.
Thanks, - Mark
