Global optimization of biomolecules using AMBER9

Here you can find examples of input files necessary to work with GMIN:

1. coords.inpcrd -- file with coordinates

2. coords.prmtop -- topology file (see here)

3. min.in -- file with AMBER9 keywords describing the conditions for AMBER minimization of the studied system, however in this particular case AMBER9 calculates only energy of the system, e.g.:

  # Minimization Parameters
  &cntrl
     imin   = 1,
     ncyc = 1,
     maxcyc = 1,
     igb = 2, saltcon=0.1,
     ntb    = 0,
     cut = 8.22,
     rgbmax = 8.22,
     ifswitch = 1,
   /

4. min_md.in -- this file controls conditions for molecular dynamics in AMBER9, e.g.:

  # MD  Paramaters
  &cntrl
     imin = 0,
     tempi = 0.0, temp0 = 400.0,
     ntt = 3, gamma_ln = 10.0,
     nstlim = 500, dt = 0.001,
     igb = 2, saltcon = 0.1,   
     ntb = 0,nscm=0,
     ntc = 2,ntf = 2, 
     ntpr = 500, ntwx = 500, ntwr=500, 
     nrespa=1,
     cut = 8.22,
     rgbmax = 8.22,
     ifswitch = 1,
  /

5. data -- file with GMIN keywords:

  SLOPPYCONV 1.0D-6
  TIGHTCONV  1.0D-7
  MAXERISE   1.0D-4
  MAXIT      100 600
  MAXBFGS    1.0
  SAVE       100
  STEPS      1000
  STEP       0.0
  RADIUS     300
  AMBERMDSTEPS
  AMBER9 coords.inpcrd inpcrd

Thats all for the beginning!