packmol command not found

Introduction

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

packmol: command not found

or when using sudo you get the following error message

sudo: packmol: command not found

Solutions to packmol: command not found

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

In Ubuntu packmol is provided by packmol package.

packmol is:

Initial configurations for Molecular Dynamics Simulations by packing optimization.

Packmol creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The packing guarantees that short range repulsive interactions do not disrupt the simulations.

The great variety of types of spatial constraints that can be attributed to the molecules, or atoms within the molecules, makes it easy to create ordered systems, such as lamellar, spherical or tubular lipid layers.

The user must provide only the coordinates of one molecule of each type, the number of molecules of each type and the spatial constraints that each type of molecule must satisfy.

The package is compatible with input files of PDB, TINKER, XYZ and MOLDY formats.

See http://m3g.iqm.unicamp.br/packmol for more information.

References

Please always cite one of the following references in publications for which Packmol was useful:

L Martinez, R Andrade, EG Birgin, JM Martinez, Packmol: A package for building initial configurations for molecular dynamics simulations. Journal of Computational Chemistry, 30, 2157-2164, 2009. (http://www3.interscience.wiley.com/journal/122210103/abstract)

JM Martinez, L Martinez, Packing optimization for the automated generation of complex system’s initial configurations for molecular dynamics and docking. Journal of Computational Chemistry, 24, 819-825, 2003. (http://www3.interscience.wiley.com/journal/104086246/abstract)

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

sudo apt-get -y install packmol

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

You can also use apt command to install packmol.

sudo apt -y install packmol

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

sudo aptitude install packmol

Summary

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