Dear Amber Users:
We are simulating an 11mer DNA duplex with AMBER9 and willing to compute the free energy of the DNA central 5mer by MM-PBSA. I am aware that the MM-PBSA has a ligand and receptor selection function to compute the binding energy. However, the DNA central 5mer is covalently linked to the rest of DNA. So the MM-PBSA does not simply work for this problem. Is there an easy way to computer the part DNA's free energy? Thank you very much for the help!
Lei Jia
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Received on Wed Dec 05 2007 - 06:07:19 PST
