obfitall command not found

In this troubleshooting guide we learn how to fix obfitall command not found error message

Introduction

When you run more command in linux terminal / console, you get the following error message

obfitall: command not found

or when using sudo you get the following error message

sudo: obfitall: command not found

Solutions to obfitall: command not found

How To Fix obfitall: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu obfitall is provided by openbabel package.

openbabel is:

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It allows one to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Features include:

  • Hydrogen addition and deletion
  • Support for Molecular Mechanics
  • Support for SMARTS molecular matching syntax
  • Automatic feature perception (rings, bonds, hybridization, aromaticity)
  • Flexible atom typer and perception of multiple bonds from atomic coordinates
  • Gasteiger-Marsili partial charge calculation

File formats Open Babel supports include PDB, XYZ, CIF, CML, SMILES, MDL Molfile, ChemDraw, Gaussian, GAMESS, MOPAC and MPQC.

This package includes the following utilities:

  • obabel: Convert between various chemical file formats
  • obenergy: Calculate the energy for a molecule
  • obminimize: Optimize the geometry, minimize the energy for a molecule
  • obgrep: Molecular search program using SMARTS pattern
  • obgen: Generate 3D coordinates for a molecule
  • obprop: Print standard molecular properties
  • obfit: Superimpose two molecules based on a pattern
  • obrotamer: Generate conformer/rotamer coordinates
  • obconformer: Generate low-energy conformers
  • obchiral: Print molecular chirality information
  • obrotate: Rotate dihedral angle of molecules in batch mode
  • obprobe: Create electrostatic probe grid

To fix this problem, we can install more using the command below.

sudo apt-get -y install openbabel

This command might take some time to finish depending on your machine internet connection.

You can also use apt command to install openbabel.

sudo apt -y install openbabel

Or if you have aptitude installed you can use the following command.

sudo aptitude install openbabel

Summary

In this tutorial we learn how to fix obfitall command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.