Re: [AMBER] question

From: . mirage <m.o.m.live.fr>
Date: Wed, 29 Jan 2014 14:39:13 +0000

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
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