AMBER Archive (2006)

Subject: Re: AMBER: Not getting proper structure after minimization

From: Carlos Simmerling (
Date: Tue Oct 24 2006 - 16:06:14 CDT

you don't say what the initial model looks like before using Amber.
does it have the right structure?

Dave, Sonya wrote:

> Hello,
> I am trying to make a structure of a protein. I have the crystal
> structure of a related protein, and the sequence of my protein. I
> had InsightII calculate a homology comparision. I am now trying to
> minimize that protein, to get the final structure.
> We are generally very confident this protein contains a motif called
> the CBS domain. This is, in the following order, beta sheet - alpha
> helix - beta sheet -beta sheet -alpha helix. PFam agrees it has this
> motif. However, when I minimize, I can not get this order to show
> up. I am only modeling the CBS domain of the protein, so that domain
> is basically all of the structure. I am very tempted to believe I am
> doing something wrong modeling, rather then that the protein does not
> contain the domain.
> Any ideas of how I can improve or change my model? I know this is a
> VERY broad question, but I have very little experience modeling, and
> would appreciate suggestions.
> Here is what I am doing.
> I always use a cutoff of 12 um.
> 1. Minimize molecule in vacuum (steepest descent 500 cycles, 100K
> cycles with steepest descent, followed by conjugate. done per tutorial)
> 2. Put molecule in octahedral box of size 25um.
> 3. Hold protein fixed, and minimize water.
> 4. Minimzation of 500 cycles, with water fixed (per tutorial).
> 5. Minimization with whole system.
> 6. Molecular dynamics with weak restraints on protein.
> 7. Molecular dynamics without restraints (100Kcycles)
> I get a structure with linker regions, and 2 alpha helixes followed by
> 2 beta helixes.
> Basically, I am following the tutorial, except minimizing in vacuum
> before putting in a water box.
> The final product shows potential energy stabilized between -276000
> and -277000
> The RMSd from the original structure is stable, around 2 A.
> The movie of the last molecular dynamics shows the atoms are still
> moving around at the last stage. Is this typical?
> The density stabilizes around 1.08 - 1.1 mg/ml
> To me, it looks, by all criteria a good model (Except for the part of
> the movie). So, do any of my parameter look improper, or is there
> any way I can improve this model (besides run more cycles). General
> ideas, thought, etc welcome.
> Thank you all for your help.
> Sonya

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