[gmx-users] forcing structure

[Tsjerk Wassenaar]

Hi Osmany,

You could try to use position restraints with your CA as reference
positions (though the reference should match the .tpr in terms of
number of atoms and atom order, so just change the coordinates).
Besides it's best to first go with a small force constant and increase
it later, with a subsequent MD run. O, and you want a protocol for
position restraint MD (define = -DPOSRES or -DPOSRE in the .mdp file).

Hope it helps,

Tsjerk

On 8/2/05, Osmany Guirola Cruz <osmany.guirola at cigb.edu.cu> wrote:
> Thanks Magnus, but i need more than a 3d alignament ... there are
> diferrences in the 3d structure of this PDBs.. and i want to force the
> second to fit the first one , forcing the structure in a way that CA of
> the second fit "exactly" in the same positions of the first..sorry if in
> the first mail i don't explain correctly :-)
> 
> Osmany
> 
> 
> On Tue, 2005-08-02 at 15:53 +0200, Magnus Andersson wrote:
> > > Hi people,
> > >
> > >   This is may problem :-)
> > > I have 2 PDBs of the same molecule(diferent 3d structure) but the first
> > > one only have the CA of the molecule ... then i want to force my second
> > > structure(whole protein) to fit the first(CA only) how can i do this?
> >
> > Use g_confrms, use both .pdb files as input and specify which residues or
> > CA should be aligned in two  .ndx files.
> >
> > Good luck / Magnus
> >
> > > can i use MD?
> > >
> > > Thanks
> > >
> > > Osmany.
> > >
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