(none)

[Eugene F DeRose]

Dear XPLORers,

	I am interested in carrying out molecular dynamics calculations of 
structures of CoBleomycin, an intercalating antibiotic, and DNA 
oligonucleotides, using NOE and dihedral restraints, obtained from 2D NMR 
data.  As a starting point, I have run the refine_gentle.inp protocol on 
the ideal DNA structures contained in the tutorial directory, using both 
the old and new versions of the topology and parameter files (i.e., 
topallhdg.dna and parallhdg.dna).  The old parameter and topology
files produced structures with 40-50 sugar angle violations > 5 degrees.  
The structures obtained with the new files had a large number of bond
( > 0.05 Angstroms), angle ( > 5 degrees), and improper ( > 5 degrees)
violations involving the sugars.

	I am puzzled as to why these calculations are producing these
violations.  Does anyone have an explaination for this?

Thanks in advance,

Eugene    
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Eugene F. DeRose        Department of Chemistry
Manager NMR Laboratory  University of Wisconsin-Milwaukee
			P.O. Box 413
			Milwaukee, WI 53211-3029
ederose at csd.uwm.edu
voice: 414-229-5896     fax: -5530
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