AMBER Archive (2004)

Subject: AMBER: positive binding free energy

From: hj zou (
Date: Thu Mar 11 2004 - 07:59:09 CST

>This is possible. I am not sure that Docking was the step that lead to
>the problem. Nevertheless, we might be more helpful if you can provide
>a bit more detailed information, like how did you do the simulations,
>the main features of the ligand and protein, the typical values of the
>individual energy terms (and the uncertainty of them).
>I doubt methods like MM/PBSA is this sensitive to the specifics of a
>force field, assuming you did the right thing for ligands. By the way,
>how did you obtain the ligand model? We are typically very shy on
>questions like "My results are wrong. Please help me to get it right."

   The process of simulation is described here.First, I calculated the binding free energy of crystal complex.The result:MM/PBSA=-30.TSTOT=-22 was consistent with available experimental evidence well.In order to calculate another ligand which was believed to be able to bind to this protein through biochemical experiment(no crystal structure available),a combination of DOCK and amber was employed.
   The structure of ligand was sketched by using sybyl SKETCH module,and then the ligand was subjected to energy minimization in sybyl using steepest descent to the gradient tolerance of 0.05kcal/mol.The optimized ligand was docked into the binding pocket which was produced by the known crstal complex by using DOCK 4.0.The highest-ranking structure of DOCK was employed to perform amber optimizaton , equlibration ,mm/pbsa and nmode calculation.The parameters and conditon of this cycle of simulation were totally the same with prior simulation.The same simulation was also performed on several other docked structures which had quite different binding modes.Nevertheless,the results made no difference(still positive).
The structure of liand is shown here:
     O O
     || ||
          | |
   The structure of protein is barrel-shaped which is composed of ten beta sheets and two alpha helices.
best regards

> Dear amber users$B!$(B
> Thanks a lot,Dr. Holger.
> As suggested by Dr. Holger,I have tried sevaral docked
> structures.Unfortunately,all of the total binding free
> energies were positive.Someone told me that amber forcefield
> sometimes does not deal with the small molecule well.Is that
> a good explanation?
> If the docked structure is not appropriate,how can I get
> the complex structure(I have tried Dock,Autodock and
> Flexx).Any other methods?
> Any suggestions are appreciated.
> Best regards

> >
> > Dear amber users$B!$(B
> > I'm performing mm-pbsa and nmode calcultion on a docked
> protein-ligand complex.
> > The mm-pbsa result:PBTOT=-13.50,The nmode
> result:TSTOT=-23.45.So the binding free energy is a positive
> value.That's impossible.The ligand binds to the protein with
> a Kd of 47.3nM(experimental measurements). Why?
> > Can anyone give me some suggestions?
> Holger:
> >Considering that several large terms add up to a usually
> small binding
> >free energy, it is very hard to tell what might have gone wrong here.
> >Since you write below that a crystal structure has worked but your
> >docked complex hasn't, a first guess might be that your
> ligand binding
> >mode obtained by docking isn't the appropriate one?!
> best regards

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to