AMBER Archive (2006)

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

From: Dave, Sonya (
Date: Tue Oct 24 2006 - 17:46:45 CDT


Before minimization, the structure has the following shape: alpha -beta - beta - alpha -alpha

Pardon my ignorance, but I'm not sure what you mean by parameter sets. To add the waters I use leap, specifically leaprc.ff99.
Is that what you were looking for, or did you mean the input files or something else? I could send you all the input files I use if that is helpful.

The homology modeling does work. I did model it with the closest one I have.

Maybe this is of use to the problem. Can the size of the water box have a significant effect on the final molecule? With a related protein (let's call this cbs1, and the one I described earlier cbs 2), using 8 um water box (instead of 25 um) I did get my domain pattern (B-a-B-B-a). Both cbs 2 and 1 should have the B-a-B-B-a pattern. Although I used 8 um water box, I used 12 um cutoff. I then read that water box must be at least 2x cutoff, so I increased waterbox to 25, and did not get the desired secondary structure pattern for either cbs 1 or 2.

Thank you for your help.

-----Original Message-----
From: on behalf of Elijah Gregory
Sent: Tue 10/24/2006 4:39 PM
Subject: Re: AMBER: Not getting proper structure after minimization
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 =/


On 10/24/06, Gustavo Seabra <> 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 <> 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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