Hi Emma, That example does not have sterics turned on. It is merely intended to make sure you have installed MMB correctly (which you have). Try exercise 1 to see an example that includes de-clashing. If you tell me more about your problem I can help guide you to use MMB most effectively. Are you interested in an MMB workshop? We are running one soon in Uppsala, and I have been thinking about setting one up in Gothenburg (thought that might be some time from now). Sam

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Today's Topics:

1. Tutorial problem - Unrealistic RNA structure generated (Emma Eriksson)

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Message: 1 Date: Tue, 4 Sep 2012 07:31:26 +0000 From: Emma Eriksson <emma.eriksson@chem.gu.se> Subject: [RNABuilder-help] Tutorial problem - Unrealistic RNA structure generated To: "rnatoolbox-help@simtk.org" <rnatoolbox-help@simtk.org> Message-ID: <E7E706508AD8CC4CA0E362089D784E9C0351AF@thane.ita.chalmers.se> Content-Type: text/plain; charset="iso-8859-1"

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