Re: [AMBER] mmgbsa for ternary system

From: Amor San Juan <>
Date: Thu, 8 Jul 2010 03:23:16 -0700 (PDT)

Hi Jason,

Thanks for the clearer explanation to me. It was helpful.

Getting the correct value for [A+C]+B using mmgbsa has a sense as what you said. I dont have an experience tracking down the error in mmgbsa by step-by-step method.

People in amber forum, I believe, has encountered this problem many times in history. Some people were successful in tracking the error, but no one has ever posted it back in the forum how they did it step-by-step. And no one in our research group has ever did it as well.


--- On Wed, 7/7/10, Jason Swails <> wrote:

From: Jason Swails <>
Subject: Re: [AMBER] mmgbsa for ternary system
To: "AMBER Mailing List" <>
Date: Wednesday, 7 July, 2010, 10:15 PM


In theory, that approach is as correct as the MM/GBSA method can be.
There's no need to do a separate trajectory for the other complex, since at
the end of the day, as I understand what you're doing, the two complexes are
the same.

To actually run MM/GBSA, you'll need 5 topology files.  Complex topology
file (A+B+C), receptor topology file 1 (A+B), receptor topology file 2
(A+C), ligand topology file 1 (C), and ligand topology file 2 (B).  You'll
also need to make sure that the trajectory files and/or frames spit out by or are consistent with your topology files.  This is
easily done by loading them into VMD or pymol or something of the like and
seeing if they look funny.  Also note that you need to look at multiple
frames to make sure that not just the first frame is OK.

Hope this helps,

On Wed, Jul 7, 2010 at 6:42 AM, Amor San Juan <> wrote:

> 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
> [A+B]+C
> complex=[A+B]+C
> receptor=A+B
> ligand=C
> [A+C]+B
> complex=[A+B]+C
> receptor=A+C
> 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?
> Amor
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
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Received on Thu Jul 08 2010 - 03:30:07 PDT
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