AMBER Archive (2006)

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

From: Gustavo Seabra (
Date: Tue Oct 24 2006 - 16:28:27 CDT

Did you try with different parameter sets, and still get similar
results? You didn't mention what parameter set you are using. I wonder
how much those results could be biased by the parameters used...


On 10/24/06, 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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