[AMBER] freezing selected residues

From: Senthil Natesan <sen.natesan.yahoo.com>
Date: Fri, 30 Apr 2010 10:11:20 -0700 (PDT)

Hi Amber users,

I am trying to minimize a protein-ligand complex, solvated with TIP3P water (8.0 A).
I want to restrain atoms that are 8 A beyond some selected binding site residues.
Earlier I used ntr=1 (with force constant 500.0 during minimization and 10.0 during MD)
for restraining protein-ligands during solvent equilibration using group list as follows

&cntrl 
----
----
/
Hold the protein and ligand 
500.0
RES 1-284 (both protein and ligand)
END
END
it worked well. Now I am not sure how to mention the distance in these inputs.
For example I want to freeze all atoms(residues & water) that are beyond 8 A of
residues 1-3, 4-12. Can someone please tell me how the input should look like?
thanks,
Senthil Natesan
      
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Received on Fri Apr 30 2010 - 10:30:04 PDT
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