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?

Much Thanks,
Jim


Molecular Engineering Laboratory University of Washington