Minimizing a structure using OPTIM and AMBER9

To optimize a geometry you need four (or five, see below) files with names specified in the following list:

1. coords.inpcrd -- file with coordinates in AMBER9 format

2. coords.prmtop -- AMBER9 topology file (see description here

3. min.in - file with AMBER9 keywords describing the conditions for molecular dynamics of the studied system, e.g.:

  Minimization
  &cntrl
     imin=1, maxcyc=1, ncyc=1,
     igb=2, saltcon=0.2,
     ntx=1, ntb=0,
     cut=15.0, rgbmax=12.0, ifswitch=1
   /

4. odata -- file with OPTIM keywords specifying method of minimization, convergence criterion, etc. e.g.:

  BFGSMIN 1.0D-6
  BFGSSTEPS 10000
  UPDATES 10
  MAXERISE 1.0D-4
  AMBER9 coords.inpcrd inpcrd

If the file for the starting geometry contains three columns with x, y, z coordinates, respectively, name this file start and change the last line of mentioned above odata file into:

  AMBER9 start

You still need to have a coords.inpcrd file in the same directory or OPTIM won't run!