From: Simon Sharpe (ssharpe_at_speck.niddk.nih.gov)
Date: Thu Feb 05 2004 - 14:13:31 CST
Hi,
I have been attempting to apply dihedral and distance restraints to a
protein within a NAMD simulation. I would like to apply these restraints
during minimization/equilibrium runs. I have tried variations on the
following script within the .conf file (increasing the value of kf,
bound/fixed restraints), but the restraints are not being applied. Can
anyone tell me what is missing here?
freeEnergy on
freeEnergyConfig {
urestraint {
dist (U, 13, C) (U, 13, CG) kf=20 ref=3.85
dist (U, 11, C) (U, 13, CD) kf=20 ref=3.4
dist (U, 12, C) (U, 13, CG) kf=20 ref=4.3
dihe (U, 11, C) (U, 12, N) (U, 12, CA) (U, 12, C) barr=20 ref=74
dihe (U, 12, N) (U, 12, CA) (U, 12, C) (U, 13, N) barr=20 ref=12
dihe (U, 12, C) (U, 13, N) (U, 13, CA) (U, 13, C) barr=20 ref=-96
dihe (U, 13, N) (U, 13, CA) (U, 13, C) (U, 14, N) barr=20 ref=124
dihe (U, 13, C) (U, 14, N) (U, 14, CA) (U, 14, C) barr=20 ref=-100
dihe (U, 14, N) (U, 14, CA) (U, 14, C) (U, 15, N) barr=20 ref=119
}
}
Thanks,
Simon
__________________________________
Simon Sharpe
Laboratory of Chemical Physics, NIDDK
National Institutes of Health
9000 Rockville Pike
Bethesda, MD 20892
_________________________________
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