dihedral constraints

Carolyn A. Kanagy checak at CHEMIND2.GSU.EDU
Fri Feb 23 16:59:41 EST 1996


I am modeling a drug bound in the minor groove of DNA 
and find that I need to place lots of constraints on
the DNA.  Two places where I want to constrain dihedrals
are the C1'-C2'-C3'-C4' torsion angle in the furanose
rings and the C6-N1-N3-C4, etc torsion angles extending
from the base of one strand into the planar base of the
other.  My question:  In the case of the sugar rings,
should I just constrain them all to -35 degrees, or should
I keep them at the original angles which range from -30 
to -40 degrees?  Same question for the inter-strand
dihedrals:  use actual starting values, or just con-
strain them all to 0 or 180 degrees?

Thanks,
Carolyn Kanagy
GSU Chemistry





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