Minimizing a structure using OPTIM and AMBER9

For users of AMBER9:

There is a list of necessary files for optimization of geometry:

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=10.0, rgbmax=8.5, 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.