[gmx-users] Again on restrained EM

Ivano Eberini Ivano.Eberini at unimi.it
Tue Apr 30 18:36:06 CEST 2002

Dear all,
as I told you in my previous mail, I am trying to follow a multistep EM 
protocol 'in vacuo' for a protein obtained by homology modelling.
I need to run, as first step, a steepest descent EM with all atoms of 
the backbone and active site residues held fixed (i.e., a side chain 
minimization), so I was wondering if I could use a posre.itp file 
containing all the backbone and active site atoms with an isotropic 
constant force (1000 kJ mol^-1 nm^-2).

[ position_restraints ]
; atom  type      fx      fy      fz
      1     1  1000.0  1000.0  1000.0

Is it correct or have I got to follow another procedure?
I apologize if this is a trivial question, but I am an absolute beginner.
Thanks and best regards,


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