"obminimize" - Optimize Geometry/Energy of Molecule

Q

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

✍: FYIcenter.com

A

"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 
Tyrosine Molecule 2D Structure
Tyrosine Molecule 2D Structure

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 
Tyrosine Molecule Minimized Structure
Tyrosine Molecule Minimized Structure

 

"obprobe" - Create Electrostatic Probe Grid

"obgrep" - Search Molecules using SMARTS

Other Open Babel Commands

⇑⇑ Open Babel Tutorials

2020-11-11, 186👍, 0💬