AMBER Archive (2006)

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

From: Elijah Gregory (ejgregory_at_gmail.com)
Date: Tue Oct 24 2006 - 18:12:35 CDT

Your water box should be large enough that the protein is not
'perturbed' by the periodic images of the molecule which 'exist
virtually' all around your protein. That's why you need the cutoff to
be *less than* the box size (at most half as big). But I'm not an
expert, so take anything I have to say with a grain of salt.

On 10/24/06, Dave, Sonya <sonya.dave_at_vanderbilt.edu> wrote:
>
>
>
> Hi,
>
> 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.
>
> Sonya
>
> -----Original Message-----
> From: owner-amber_at_scripps.edu on behalf of Elijah Gregory
> Sent: Tue 10/24/2006 4:39 PM
> To: amber_at_scripps.edu
> 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 =/
>
> ~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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