Dear amber users,
Recently I read one of your papers titled "Free Energy Calculations for Theophylline Binding to an RNA Aptamer: Comparison of MM-PBSA and Thermodynamic Integration Methods", which published on Biopolymers, 2003, 68, 16–34. I am very interested in the computational mutagenesis approach mentioned in your paper.
In that paper, it explained: "We first tried a simple computational mutagenesis approach for estimating the relative binding energy of theophylline analogues to the RNA aptamer. In this approach, ranking is performed on the basis of a single MD trajectory of RNA aptamer–theophylline complex. Theophylline is mutated into the desired analogues for each snapshot from the MD trajectory of the RNA aptamer–theophylline complex. An additional 2500 steps of energy minimization, of the ligand, and the region within 5 Å of theophylline (which covers all atoms of A7, C8, and A28 and side chains of U6, C22-U24, and G26), were performed before the MM-PBSA free energy analysis".
I just want to know how to succeed to do that, I think this method is very useful for large analogs and can save computational time. Could somebody explain it in detail?
Any response will be highly appreciated!
All the best,
Qinghua
fantasticqhl.yahoo.com
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Received on Wed Jan 20 2010 - 17:00:03 PST
