[RNABuilder-help] Tutorial problem - Unrealistic RNA structure generated

[Emma Eriksson]

Hi all,



I am new to the MMB software and I am going through the tutorials in order to learn how the program works. However, I am not even able to complete the first tutorial (Exercise 0 with commands.singlebasepair.dat). The files last.1.pdb and trajectory.1.pdb are generated but the RNA structure is unrealistic, with overlapping bases, like if they did not feel each other's presence. The folding to this conformation happens very early in the trajectory.

I am following the exact instructions from the tutorial and I have not made any changes. I am running on Windows 7. What am I doing wrong?

I would really appreciate some help. Thank you!



Best regards,

Emma
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