In my work with DNA simulations I have taken coordinates from .crd files, and I have used IC SEED & IC BUILD. But I have noticed that when I build ss-DNA using the later method that the initial configuration is fully extended and wonder about the following: Under what time scale can I expect a ss-DNA in explict solvent with 1M excess NaCl to come to a realistic configuration? It just occurred to me as I was posting this that I could run MC before MD, is this best or is there another way for getting good starting coordinates for a ss-DNA that is not in the databanks?
It takes quite some time (hundreds of ps) just to loose memory of the starting configuration. You may want to look at this paper:
Sen, S. and L. Nilsson (2001). "MD Simulations of Homomorphous PNA, DNA and RNA Single Strands: Characterization and Comparison of Conformations and Dynamics." J Am Chem Soc 123: 7414-7422.
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.
You could try the program NAB from Dave Case's group:www.scripps.edu/case