AMBER Archive (2009)

Subject: [AMBER] molecular mechanic minimisation with amber

From: momo momo (m-22_at_hotmail.fr)
Date: Wed Jan 14 2009 - 08:58:47 CST


Hi
 I want to do a Molecular Mechanic Energy minimisation using amber:
 
is it correct like this??
 
      sander -O -i sander.in -o sander.out -p prmtop -c inpcrd -r restrt
 
  with this sander.in
 
 initial minimisation prior to MD
  &cntrl
   imin = 1,
   maxcyc = 10000,
   ncyc = 5000,
   ntb = 0,
   igb = 0,
   ntc = 2,
   ntf = 2,
   cut = 12,
  /
 
 else? why i can do this?
Thanks
 
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