[AMBER] How do I study the dimerisation energy (i.e. energy required to form a dimer from two monomeric units) using AMBER?

From: Suchetana Gupta <tutulg.gmail.com>
Date: Sat, 29 Aug 2015 12:45:11 +0530

My protein is a homodimer of some ~100 amino acids. I wish to calculate its
energy required for dimerisation. The process that I am following is:
1. Take the dimer. Run 40ns MD. Calculate MMGBSA free energy.
2. Take a monomer. Run 40ns MD. Calculate MMGBSA free energy.
Dimerisation energy=1-(2*2)

Now doing this, I am getting less dimerisation energy for a wild type
protein than the drug resistant mutant one. Moreover, the drug resistant
variety (both monomer as well as dimer) is showing stabler energy value
than WT counterpart.

Have repeated this quite a few times.
Where am I going wrong?
AMBER mailing list
Received on Sat Aug 29 2015 - 00:30:03 PDT
Custom Search