Docking Studies in InsightII
The purpose of this workshop is to acquaint you with the interface to
InsightII and its basic commands, as well as help you set up your
DNA/RNA system for further studies.
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During this hands-on workshop you will:
- retrieve a PDB file from a database and load it into InsightII
- change some functional groups on the RNA
- add hydrogen atoms to the RNA molecule
- sketch the tether molecule and convert it to 3D
- link the tether covalently to the RNA molecule
- assign potentials
- minimize the RNA-tether molecule
- run dynamics of the RNA-tether molecule
- analyze the results
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