AMBER Archive (2006)

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

From: Elijah Gregory (ejgregory_at_gmail.com)
Date: Tue Oct 24 2006 - 16:39:08 CDT

Fit your protein of interest to the PDB of the homologous strucutre
you already know is "close-to" what you're looking for. Then do your
minimization. If that doesn't work, then you've got worse problems
than minimization to worry about =/

~Elijah

On 10/24/06, Gustavo Seabra <gustavo.seabra_at_gmail.com> wrote:
> 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...
> (Anyone??)
>
> Gustavo.
>
> On 10/24/06, Dave, Sonya <sonya.dave_at_vanderbilt.edu> 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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