[Xplor-nih] RNA-DNA Hybrid

[brinson at umbi.umd.edu]

Dear users of Xplor-nih,
             I am new to python and xplor and am trying to compute a 20bp RNA-DNA hybrid. I have included the standard restraints - base/backbone NOEs, hydrogen-bond NOEs, dihedrals, and one set of RDCs. I created a decent starting structure using the anneal.py protocol. When I input that structure into refine_full.py from /eginput/dna_refi, the helix seems to become overwound in the middle and underwound at the ends. I have tinkered with the force constants and temperature (from 3000 down to 300). I added some "anti"-noes (~20A at various locations, generated from InsightII) to try to help, but my output structures did not improve. There are no apparent errors in the output file.  I would appreciate advice on refining the structure.

Thank you,
Robert

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