Minimizing a structure using OPTIM and AMBER9

For users of AMBER9:

To optimize 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

3. min.in - file with AMBER9 keywords describing conditions for molecular dynamics of 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 1000000
  UPDATES 10000
  MAXERISE 1.0D-4
  AMBER9 coords.inpcrd inpcrd

If file with 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

Still you need to have coords.inpcrd file in the same directory.

Files coords.inpcrd and coords.prmtop are created by LEaP (program in AMBER package). In case of coords.prmtop it is important to use program perm-prmtop.py to obtain topology file invariant to permutation of chemically equivalent atoms or groups (see [description]) of it.