[gmx-users] forcing structure
Osmany Guirola Cruz
osmany.guirola at cigb.edu.cu
Tue Aug 2 16:09:56 CEST 2005
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 :-)
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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