Avoiding knotting with TAD?

Brian Smith brian at chem.ed.ac.uk
Wed Mar 28 15:10:07 EST 2001


Hi,
	If anyone has any tips on how to avoid NMR structure calculations
getting trapped in knotted states using torsion angle dynamics in CNS, I
would love to hear them.  I've tried protocols à la anneal.inp from the
standard release and also along the lines used in the ARIA protocols from
Michael Nilges' lab. My case is perhaps trickier than average - two module
fragment using plenty of ambiguous NOEs.  In the initial stages at high
temp, the two modules collapse together satisfying the NOEs, but as the
Van der Waals repulsion comes up and the modules push apart knots get
trapped - particularly the inter-modular linker sticking through the
middle of an adjacent loop.  I can calculate respectable structures using
cartesian space dynamics, but TAD is supposed to be more efficient ain't
it?

Any ideas?

Brian Smith

Dr. Brian O. Smith ----------------------- Brian.O.Smith at ed.ac.uk
Institute of Cell and Molecular Biology, University of Edinburgh, 
            King's Buildings, Edinburgh EH9 3JR, UK.
Tel: 0131 650 7051/7045/4704                   Fax: 0131 650 7055




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