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working with DNA

Purnima Khandelwal purnima at tifrc3.tifr.res.in
Tue Feb 2 10:56:27 EST 1999


I have recently started to use x-plor for structure calculation, after 
working for a while on DISCOVER (MSI).

My problem is how to do simulated annealing on a double stranded DNA 
molecule since if I do simulated annealing, the two strands tend to fly 
apart, despite of hydrogen-bond constraints between them. 

Secondly, how to put symmetric constraints for the equivalent strands of
the double helical DNA, and how much symmetry violation, in terms of
interproton distances and bond angles, is allowed? Ideally both the
strands should have identical geometries, but I have found by molecular
dynamics simulations using DISCOVER that even after giving the same
restraints for both the strands, there is some assymetry in the geometry.

Please help.

Thank you.


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