HiMy work is to do molecular dynamic for each guest separately and after that to do mmpbsa over full trajectory and in final compare the result.
the most stable orientation= the orientation which has minimum deltaG in 1:1 or in 2:1, (not the minima for one complex trajectory)
The "most stable orientation for 1:1 complex H>B" is more stable then "the most stable orientation for 1:1 complex H>A"
The "most stable orientation for 2:1 complex H>BB" is more stable then "the most stable orientation for 2:1 complex H>AA"
But out the "most stable orientation" i have somme orientation in H>A or H>AA which are more stable of H>B or or H>BB respectively
My question is, what we say that B is more stable than A (on comparing only the orientation which have the better delta G ignoring some more stable orientation A than B.
Thank's in advance for all reponse.
> From: jason.swails.gmail.com
> To: amber.ambermd.org
> Date: Wed, 29 Jan 2014 08:37:08 -0500
> Subject: Re: [AMBER] question
>
> On Mon, 2014-01-27 at 13:04 +0000, . mirage wrote:
> > Hi amber user'sin order to study a comlexes type hote:invited 1:1 and
> > 2:1 by calculating mmpbsa energy I chose one type on hote molecule (H)
> > and two types of guest (A or B). we have then H>A, H>B, H>AA and H>BB
> > For each type of complex, the guest B has the most stable orientations
> > (minimum deltaG), but it has also some stable orientations A than B.
> > My question is, what we say that B is more stable than A (on comparing
> > only the orientation which have the minimum delta G ignoring some more
> > stable orientation A than B.Thank's in advance for all reponse.
>
> I'm not sure I understand the question. It seems that you have a host
> that has two binding sites that can bind one of two guests; A or B. It
> seems that the host can bind with either one or two of the guests, but
> not one of each guest (i.e., not H>AB or H>BA), presumably because they
> are never mixed together, I'm not sure. You ran molecular dynamics (I
> am assuming) on these complexes and then performed MM/PBSA analyses on
> the trajectories and got energies.
>
> An important distinction: a single orientation is NOT a Delta G. Free
> energies are ensemble averages over a Boltzmann-weighted distribution.
> Simply discarding snapshots because they don't fit your expectations is
> not a good approach. If you want to make some comparison of stability,
> it is not the "lowest energy" snapshots you should be comparing, it is
> the full ensemble averages.
>
> If you have not run molecular dynamics simulations to generate the
> snapshots you used for MM/PBSA and instead used something like docking
> poses you got from some docking program then this is different. Docking
> does not generate a proper Boltzmann-weighted distribution so you can
> never be quite sure how to weight each orientation. In this case you
> may be able to make an argument to discard unfavorable poses, but
> ultimately such choices will be based on subjective evaluations and
> hand-waving.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Wed Jan 29 2014 - 07:00:02 PST
