Homodimer Simulations do not output Free Energy

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Joined: 06/08/2011


I've been using the web form to calculate homodimer simulations (http://mfold.rna.albany.edu/?q=DINAMelt/Homodimer-simulations) both manually and through POST requests but the data returned does not contain a free energy (delta G) value. Am I doing something wrong? I've tried the hybridization of 2 strands form as well but since they both submit to the same page, it makes sense that they're both having the same issue.

Sequence 5'--3': ACGAAAGAGTA

Temperature range From 16°C by 1°C to 50°C

NA type DNA

Initial concentrations [A0]: 2 Units: uM

Salt conditions [Na+]: 15 [Mg++]: 1.5 Units: mM

-Thanks, Christine

Joined: 11/12/2010
Lack of deltaG value for hybridization simulations

You are correct. To my amazement, ΔG has never appeared on the primary output page of the "full service" DINAMelt web server. It now does. For your information, ΔG is the difference between the free energies at Tmin and Tmax that can be found in the file A-B.ens.dG (for hetero-dimer simulations) or A-A.ens.dG (for homo-dimer simulations). These files can be accessed by downloading the entire job or by adding the name of the file to the custom URL for the output at the top of your browser. Thank you for pointing out this omission.