What Is "obminimize" command? How to use it to optimize the geometry and minimize the energy for a given molecule?

"obminimize" command is a command line tool provided in the Open Babel package that allows you to optimize the geometry and minimize the energy for a given molecule.

Here is the user manual of the "obminimize" command.

NAME
     obminimize -- optimize the geometry, minimize the energy for a molecule

SYNOPSIS
     obminimize [OPTIONS] filename

DESCRIPTION
     The obminimize tool can be used to minimize the energy for molecules inside (multi-)molecule files (e.g., MOL2,
     etc.)

OPTIONS
     If no filename is given, obminimize will give all options including the available forcefields.

     -n steps
           Specify the maximum number of steps (default=2500)

     -cg   Use conjugate gradients algorithm (default)

     -sd   Use steepest descent algorithm

     -c criteria
           Set convergence criteria (default=1e-6)

     -ff forcefield
           Select the forcefield

EXAMPLES
     View the possible options, including available forcefields:
          obminimize
          
     Minimize the energy for the molecule(s) in file test.mol2:
          obminimize test.mol2
    
     Minimize the energy for the molecule(s) in file test.mol2 using the Ghemical 
     forcefield:
          obminimize -ff Ghemical test.mol2
    
     Minimize the energy for the molecule(s) in file test.mol2 by taking at most 
     300 geometry optimization steps
          obminimize -n 300 test.mol2
    
     Minimize the energy for the molecule(s) in file test.mol2 using the steepest 
     descent algorithm and convergence criteria 1e-5:
          obminimize -sd -c 1e-5 test.mol2

Here is an example of minimizing the tyrosine molecule with the "obminimize" command:

1. Create a 2D structure of the tyrosine molecule:

fyicenter$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -O tyrosine.sdf --gen2D
1 molecule converted

fyicenter$ babel tyrosine.sdf tyrosine.svg
1 molecule converted
29 audit log messages 

2. Optimize the geometry and minimize the energy of the tyrosine molecule. Note that "obminimize" command creates the output molecule in PDB format.

fyicenter$ obminimize tyrosine.sdf > tyrosine-minimized.pdb

A T O M   T Y P E S
IDX  TYPE
1  0603
2  0603
3  0603
4  0603
5  0603
6  0603
7  0600
8  0600
9  0601
10  0801
11  0800
12  0700
13  0800

C H A R G E S
IDX  CHARGE
1  0.000000
2  0.000000
3  0.000000
4  0.000000
5  0.000000
6  0.000000
7  0.000000
8  0.000000
9  0.100000
10  -0.100000
11  0.000000
12  0.000000
13  0.000000

S E T T I N G   U P   C A L C U L A T I O N S

SETTING UP BOND CALCULATIONS...
SETTING UP ANGLE CALCULATIONS...
SETTING UP TORSION CALCULATIONS...
SETTING UP VAN DER WAALS CALCULATIONS...
SETTING UP ELECTROSTATIC CALCULATIONS...

C O N J U G A T E   G R A D I E N T S
STEPS = 2500
STEP n     E(n)       E(n-1)    
--------------------------------
    1    10225.625    10903.871
    2    7582.300    7582.300
    CONJUGATE GRADIENTS HAS CONVERGED
Time: 0seconds. Iterations per second: inf

3. See what the minimized molecule structure looks like:

fyicenter$ babel tyrosine-minimized.pdb tyrosine-minimized.svg 
1 molecule converted
28 audit log messages 

⇒ "obprobe" - Create Electrostatic Probe Grid

⇐ "obgrep" - Search Molecules using SMARTS

⇑ Other Open Babel Commands

⇑⇑ Open Babel Tutorials