[AMBER] Defining restraint by distance

From: Olotu Odunayo <paxoo.nottingham.ac.uk>
Date: Wed, 18 Aug 2010 09:19:26 +0100

Hi, I was wondering if anyone can help.
 
I want to run MD simulation on a protein-ligand complex, and restrain residues and water molecules 10A away from the ligand, does anyone know how to define this?
 
I know the residues and can do something like this, but I'm not sure how to include the water molecules in this region that leap added for me.

Minimise 2H7I.25778
 &cntrl
  imin=1,
  maxcyc=1000, ncyc=500,
  ntb=1, cut=10.0,
  ntc=2, ntf=2,
  ntpr=100,
  ntr=1, restraint-wt=2.0
  restraintmask=':1-17,22-61,67-100,104-144,150-153,159,170-195,220-268'
 /

Thanks
O. Loyin
                                                                     

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Received on Wed Aug 18 2010 - 01:30:04 PDT
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