Thank you. I read your article. In your article, you state "We first generated the atomic coordinates of the single-stranded DNA in B-form..." You mentioned having used Insight II. I am using the academic version of CHARMM (27b4 & 30b1). I would like to know if there are CHARMM scripts available to build coordinates in B-form, A-form, Z-form, etc. given an arbirtrary sequence. When I use IC SEED & IC BUILD I get a fully extended, non-helical form.
Molecular Engineering Laboratory
University of Washington