Dear AMBER users,
Now I'm studying a protein by MD simulations, this protein have three domains of A, B and C, one loop in A (call auto-inhibition-loop, AIL) interacted with a few residues in C and formed a so-called “auto-inhibition” state. I introduce a mutation at one interacting site in C and have finished 20ns MD simulations for both wild-type and mutant. Now I want to get the interaction energy of AIL with those residues in domain C from both MD trajectories, here is some questions:
1). Can I achieve the objective based on already finished classical MD simulations through some post-process, such as MM_PBSA/GBSA?
2). If I can get this type of interaction energy through MM_PBSA/GBSA, then how will I set input values in mm_pbsa.in, especially for COMPT/RECPT/LIGPT in .GENERAL section, and corresponding residue numbers in .DECOMP section? Supposing the organization of this protein is like:
Domain A: 1 ~ 100
AIL: 60 ~ 70
Domain B: 101 ~ 200
Domain C: 201 ~ 600
3). To get the total interaction energy of AIL with nearby residues in domain C, which type of energy decomposition is better for summing up, per-residue or pairwise per-residue? Which value is the best for DCTYPE?
4). If I can’t get this interaction energy based on finished MD simulations, can I get it by running other MD simulations in Amber9? Then which key parameters should I modify?
5). Even if the answer of 4) is “No”, could you give me some suggestions on how to compare the “binding affinity” of AIL to domain C in wild-type and mutant through computational technique?
Thanks in advance, and I really, greatly appreciate any advice!
Zhihong
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Received on Tue May 18 2010 - 16:30:03 PDT
