"obenergy" - Calculate Molecule Energy

Cheminformatics Tutorials - Herong's Tutorial Examples

∟Command Line Tools Provided by Open Babel

∟"obenergy" - Calculate Molecule Energy

This section provides a quick introduction on the 'obenergy' command provided in Open Babel package to calculate molecule energy.

What Is "obenergy" Command? "obenergy" command is a command line tool provided in the Open Babel package that allows you to Calculate Molecule Energy.

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

NAME
     obenergy -- calculate the energy for a molecule

SYNOPSIS
     obenergy [OPTIONS] filename

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

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

     -v    Verbose: print out all individual energy interactions

     -ff forcefield
           Select the forcefield

EXAMPLES
     View the possible options, including available forcefields:
           obenergy

     Calculate the energy for the molecule(s) in file test.mol2:
           obenergy test.mol2

     Calculate the energy for the molecule(s) in file test.mol2 using the
     Ghemical forcefield:
           obenergy -ff Ghemical test.mol2

      Calculate the energy for the molecule(s) in file test.mol2 and print out
     all individual energy interactions:
           obenergy -v test.mol2

Here is an example of calculating molecule energy using the "obenergy" command using the default force field type:

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

herong$ obenergy tyrosine.sdf

A T O M   T Y P E S
IDX  TYPE
1  C_R
2  C_R
3  C_R
4  C_R
5  C_R
6  C_R
7  C_3
8  C_3
9  C_2
10  O_2
11  O_2
12  N_3
13  O_2

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 OOP CALCULATIONS...
SETTING UP VAN DER WAALS CALCULATIONS...

E N E R G Y
     TOTAL BOND STRETCHING ENERGY = 4001.440 kJ/mol
     TOTAL ANGLE BENDING ENERGY =   66.916 kJ/mol
     TOTAL TORSIONAL ENERGY =    8.872 kJ/mol
     TOTAL VAN DER WAALS ENERGY = 9731.431 kJ/mol

TOTAL ENERGY = 13808.65839 kJ/mol