Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
"obminimize" - Optimize Geometry/Energy of Molecule
This section provides a quick introduction on the 'obminimize' command provided in Open Babel package to optimize geometry and energy of molecules.
What Is "obminimize" command? - "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:
herong$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -O tyrosine.sdf --gen2D 1 molecule converted herong$ obabel tyrosine.sdf tyrosine.svg 1 molecule converted
2. Optimize the geometry and minimize the energy of the tyrosine molecule. Note that "obminimize" command creates the output molecule in PDB format.
herong$ 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:
herong$ obabel tyrosine-minimized.pdb tyrosine-minimized.svg 1 molecule converted
Table of Contents
SMILES (Simplified Molecular-Input Line-Entry System)
Open Babel: The Open Source Chemistry Toolbox
Using Open Babel Command: "obabel"
Generating SVG Pictures with Open Babel
Substructure Search with Open Babel
Similarity Search with Open Babel
Fingerprint Index for Fastsearch with Open Babel
Stereochemistry with Open Babel
►Command Line Tools Provided by Open Babel
List of Open Babel Command Line Tools
"obchiral" - Print Chirality Information
"obconformer" - Generate Best Conformer
"obenergy" - Calculate Molecule Energy
"obfit" - Superimpose Two Molecules
"obgen" - Generate Molecule 3D Structures
"obgrep" - Search Molecules using SMARTS
►"obminimize" - Optimize Geometry/Energy of Molecule
"obprobe" - Create Electrostatic Probe Grid
"obrotamer" - Generate Random Rotational Isomers
"obrotate" - Rotate Dihedral Angles with SMARTS
RDKit: Open-Source Cheminformatics Software
rdkit.Chem.rdchem - The Core Module
rdkit.Chem.rdmolfiles - Molecular File Module
rdkit.Chem.rdDepictor - Compute 2D Coordinates
rdkit.Chem.Draw - Handle Molecule Images
Molecule Substructure Search with RDKit
rdkit.Chem.rdmolops - Molecule Operations
Daylight Fingerprint Generator in RDKit
Morgan Fingerprint Generator in RDKit
RDKit Performance on Substructure Search
Introduction to Molecular Fingerprints
OCSR (Optical Chemical Structure Recognition)
AlphaFold - Protein Structure Prediction