Global optimization of biomolecules using AMBER9 with Structural Restraints

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
  &cntrl
    imin=1, maxcyc=1, ncyc=1,
    igb=2, saltcon=0.2,
    ntx=1, ntb=0,
    cut=999.0
  /

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

  STOP
   &cntrl
    imin = 0,
    tempi = 500.0, temp0 = 700.0,
    ntt = 3, gamma_ln = 1.0,
    nstlim = 300, dt = 0.001,
    igb = 2, saltcon = 0.2,
    ntb = 0,
    ntpr = 100, ntwx = 100, nrespa=1,
    cut = 999.0
  /

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!