Minimizing a structure using OPTIM and AMBER9

For users of AMBER9:

There is a list of necessary files:

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,
   cut=10.0, igb=2, saltcon=0.2,
   ntx=1, ntb=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

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