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Molecular dynamics · PyMOL

ProBiS H2O MD Plugin

Identify conserved water molecules in molecular dynamics trajectories and visualize them in PyMOL.

Get the software Installation guide

Downloads

ProBiS H2O MD Plugin

Example Input Files

The below example molecular dynamics files (PDB and DCD) were generated using CHARMM biomolecular simulation program. A PDB file is needed to get topology and coordinates of a protein (note: we do not use PSF files) and the DCD file contains the trajectory of a protein in a water box.
Versions and Release Notes

1.0.3 (Nov/12/2025)

  • Psf file for topology instead of pdb: this is necessary since pdb files are not suited for large numbers of waters
  • Fixed water heavy atom recognition in pdb file if residue is HOH

1.0.2 (Mar/09/2025)

  • Fixed automatic installation of python packages (MDAnalysis and scikit-learn) which failed previously
  • For changes to come into effect, RESTART PYMOL after installation is complete

1.0.1 (Apr/13/2023)

  • Added Mac support (for M2 processor)
  • Fixed a water clustering problem

1.0.0 (Mar/16/2022)

  • Works on Linux and Windows

Overview

ProBiS H2O MD plugin for PyMOL enables identification of conserved water molecules from molecular dynamics (MD) trajectories of proteins in water. The picture below shows several identified conserved waters (red spheres) on a protein (white caroon model) with glycosylation (blue sticks) in a water box (white surface model).
Conserved waters on a protein detected from an MD trajectory

Installation

  • Download the ProBiS H2O MD plugin file
  • Open PyMOL and go to Plugin Manager -> Install New Plugin -> Choose file
  • Select the plugin file on your disk
  • Click Install button (ProBiS H2O MD appears in Plugins dropdown menu)
  • Click on ProBiS H2O MD in the dropdown menu to start the plugin
  • The plugin will verify if pip3 module is installed and perform automatic installation of two more packages

System Requirements

The ProBiS H2O MD plugin has been developed for Linux, Windows and Mac (from version 1.0.1 on) with PyMOL version 2.0 or higher. The plugin depends on several python packages that need to be installed for the plugin to work. First of all, pip3 (package installer for python3) needs to be installed on the system. When pip3 is installed, the plugin will - on first startup - automatically install additional python packages (scikit-learn and MDAnalysis). If installation of these packages would fail for some reason, then please install them manually (see below).

Manual installation of pip3 (Ubuntu)

apt-get install python3-pip

Manual installation of additional packages - use this if automatic installation fails (Ubuntu)

pip3 install MDAnalysis scikit-learn

Cite this software

pdf Marko Jukic, Janez Konc, Urban Bren, Dusanka Janezic. ProBiS H2O MD Approach for Identification of Conserved Water Sites in Protein Structures for Drug Design. ACS Medicinal Chemistry Letters, 2020, 11, 877-882. Full Text
MLA
Marko Jukic, Janez Konc, Urban Bren, Dusanka Janezic. ProBiS H2O MD Approach for Identification of Conserved Water Sites in Protein Structures for Drug Design. ACS Medicinal Chemistry Letters, 2020, 11, 877-882. Full Text

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