Global optimization of biomolecules using AMBER9 with Structural Restraints

This if similar to running plain global energy optimisation. Here you can find examples of input files necessary to work with GMIN:

1. coords.inpcrd -- file with coordinates

1.5 copy coords.inpcrd to refc where refc are the reference coordinates for the constraining potential

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=10.0, rgbmax=8.22
    ifswitch = 1
  /

4. min_md.in -- this file controls conditions for molecular dynamics in AMBER9, where ntr=1,restraint_wt=500.0 determines the constraints and their strength and restraintmask=':1-63' determines the residues affected. e.g.:

  STOP
   &cntrl
    imin   = 0,
    tempi = 300.0, temp0 = 500.0,
    ntt = 3, gamma_ln = 1.0,
    nstlim = 300, dt = 0.001,
    igb = 2, saltcon = 0.1,
    ntb    = 0,
    ntpr = 50, ntwx = 10,nrespa=1,
    cut    = 10.0,rgbmax=8.22
    ifswitch = 1
    ntr=1,restraint_wt=500.0
    restraintmask=':1-63'
  /

5. data -- file with GMIN keywords:

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