"obenergy" - Calculate Molecule Energy
What Is "obenergy" command? How to use it to Calculate Molecule Energy?
"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:
fyicenter$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -o sdf -O tyrosine.sdf --gen2D 1 molecule converted fyicenter$ 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
⇒ "obfit" - Superimpose Two Molecules
⇐ "obconformer" - Generate Best Conformer
2020-11-11, 647👍, 0💬
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