Hello Jakob--
>
> I wish to use a few angle constraints to define the orientation
> between different monomers. I guess the bondAngle term is the better
> option. Do I need to write this potential myself or is it already
> coded in an example?
ok. It's also possible using the old XPLOR angle term- and probably
easier in this case. Attached is an example of how to do this using
model.pdb from eginput/gb1_rdc.
best regards--
Charles
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import protocol
protocol.loadPDB('model.pdb',deleteUnknownAtoms=True)
import xplorPot
print xplorPot.XplorPot('ANGL').calcEnergy()
xplor.command('''
topo
presidue ang1
add angle 1CA 2CA 3CA
end
end
''')
#define the angle (CA 2) - (CA 4) - (CA 20) with equilibrium value of 120
degrees
xplor.command('''
patch ang1 refe=1=(resid 2) refe=2=(resid 4) refe=3=(resid 20) end
''')
print xplorPot.XplorPot('ANGL').calcEnergy()
xplor.command('''
param
ANGLE (resid 2 and name CA) (resid 4 and name CA) (resid 20 and name CA)
500.00 120
end
''')
print xplorPot.XplorPot('ANGL').calcEnergy()
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--
Charles Schwieters email: Charles at Schwieters.org
www: http://schwieters.org/cds
phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt
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