Hello everyone,
I study the ionization of small complexes composed of several stacked DNA bases. The values of ionization potentials seem to be very dependent of the conformational parameters. I use web-X3DNA to determine the local base step parameters (shift, slide, rise, tilt, roll and twist) of my complexes. I would understand how these parameters are determined by the software (because My results are very variable).
In that purpose, I looked for information in the tutorial and in some articles related to the program but it doesn't really help me. I've namely found that X3DNA adopts the standard reference frame for the parameters but again, it doesn't help me much. Do you have detailed information about the determination of the parameters by X3DNA or can you indicate me where I can found more precise information ?
Thank you in advance,
Nicolas (PhD student at ULB, Belgium)