AMBER Archive (2007)

Subject: AMBER: Free energy for part of the system

From: jialei (leijianyu_at_hotmail.com)
Date: Mon Dec 03 2007 - 13:12:47 CST

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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