[AMBER] mmgbsa for ternary system

From: Amor San Juan <amorsanjuan.yahoo.com>
Date: Wed, 7 Jul 2010 03:42:50 -0700 (PDT)

I digress from previous entry of questions I posted, instead ask the forum for basic knowledge or perhaps experience.

I am analyzing  system with a protein (187 residues), peptide (12 residues) and ligand (m7gtp). Now, let us say protein (A), peptide (B) and ligand (C). I perform md run for [A+B] + C (where [A+B] is receptor and C is ligand. Calculation for mmgbsa went smooth for ternary [A+B] + C.

Now I was asked to do mmgbsa calculation using the ternary  [A+B] + C trajectory to obtain a new ternary of [A+C] + B wherein, [A+C] is receptor and B is ligand. The person who asked this wants to see the effect in binding energy when peptide (treated as ligand) binds into the ligand-protein (treated as receptor) in mmgbsa input.

Is it theoretically feasible or reasonable to do mmgbsa for [A+C]+B using the trajectory from [A+B]+C? If the answer is no, then I just need to stop myself finding the "correct value" for [A+C]+B. (note that the system [A+C]+B gives -1700 value of GBTOT). Has anyone here had experience calculating mmgbsa in ternary, then try to manipulate the order of binding just to see change effects.

In mmgbsa output, there are 3 columns (complex, receptor, ligand). So, for


ligand =B

Assignment of complex is the same for both because I use the same ternary trajectory. I question if it is reasonable to assign complex [A+B]+C for system ternary [A+C]=B? I know I dont have the choice because I used the same ternary trajectory, but in theory is it correct?


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Received on Wed Jul 07 2010 - 04:00:03 PDT
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