Connect with us

Software

How to upgrade cmake on Ubuntu (Linux)?

Dr. Muniba Faiza

Published

on

How to upgrade cmake on Ubuntu/Linux?

In bioinformatics, cmake is used to install multiple software including GROMACS, jdock, and so on. Here is a short tutorial on how to upgrade cmake on Ubuntu and get rid of the previous version.

Update and upgrade your system first.

$ sudo apt-get update

$ sudo apt-get upgrade

Now check what version you have

$ cmake --version

Currently, I have 3.16. We will remove this version and then install the latest one.

Now remove this version using the following command:

$ sudo apt remove cmake -y

Let’s install the latest version.

$ pip3 install cmake --upgrade

Now check

$ cmake --version

It should display the latest version.

However, if you still see the previous version or get any error such as “could not find cmake_root !!!” like this:

CMake Error: Could not find CMAKE_ROOT !!!
CMake has most likely not been installed correctly.
Modules directory not found in
/home/user/.local/share/cmake-3.16
cmake version 3.16.3

In this case, clear the cache.

$ hash -r

Now check the version again, it should work.

$ cmake --version


 

Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba

Advertisement
Click to comment

You must be logged in to post a comment Login

Leave a Reply

Software

[Tutorial] Installing ProteStAr on Ubuntu (Linux).

Dr. Muniba Faiza

Published

on

Installing Protestar on Ubuntu

ProteStAr is a bioinformatics tool to compress protein structure files [1]. It compresses PDB/CIF files and supplementary PAE files. The compression is lossless. However, users are allowed to generate the lossy compression of files. In this article, we are installing ProteStar on Ubuntu.

(more…)

Continue Reading

Software

[Tutorial] How to install 3Dmapper on Ubuntu (Linux)?

Dr. Muniba Faiza

Published

on

Installing 3Dmapper on Ubuntu (Linux).

Understanding the relationship between genes and proteins is crucial for elucidating biological processes, and disease mechanisms, and developing targeted therapies. A new tool developed by Yang et. al., [1], provides a better solution to map annotated positions and variants to protein structures automatically. 3Dmapper is a stand-alone tool based on R and Python programming languages that map annotated genomic variants or positions to protein structures [1]. In this article, we will install 3Dmapper on Ubuntu (Linux).

(more…)

Continue Reading

Software

CMake installation and upgrade: What worked & what didn’t?!

Dr. Muniba Faiza

Published

on

CMake installation and upgrade: What worked & what didn’t?!

CMake is a widely used cross-platform build system that automates the process of compiling and linking software projects. In bioinformatics, CMake can be utilized to manage the build process of software tools and pipelines used for data analysis, algorithm implementation, and other computational tasks. However, managing the versions of CMake or upgrading it on Ubuntu (Linux) can be a trivial task for beginners. In this article, we provide methods for installing and upgrading CMake on Ubuntu.

(more…)

Continue Reading

Bioinformatics Programming

Free_Energy_Landscape-MD: Python package to create Free Energy Landscape using PCA from GROMACS.

Dr. Muniba Faiza

Published

on

In molecular dynamics (MD) simulations, a free energy landscape (FEL) serves as a crucial tool for understanding the behavior of molecules and biomolecules over time. It is difficult to understand and plot a meaningful FEL and then extract the time frames at which the plot shows minima. In this article, we introduce a new Python package (Free_Energy_Landscape-MD) to generate an FEL based on principal component analysis (PCA) from MD simulation done by GROMACS [1].

(more…)

Continue Reading

Bioinformatics News

VS_Analysis: A Python package to perform post-virtual screening analysis

Dr. Muniba Faiza

Published

on

VS_Analysis: A Python package to perform post-virtual screening analysis

Virtual screening (VS) is a crucial aspect of bioinformatics. As you may already know, there are various tools available for this purpose, including both paid and freely accessible options such as Autodock Vina. Conducting virtual screening with Autodock Vina requires less effort than analyzing its results. However, the analysis process can be challenging due to the large number of output files generated. To address this, we offer a comprehensive Python package designed to automate the analysis of virtual screening results.

(more…)

Continue Reading

Bioinformatics Programming

vs_interaction_analysis.py: Python script to perform post-virtual screening analysis

Dr. Muniba Faiza

Published

on

vs_interaction_analysis.py: Python script to perform post-virtual screening analysis

Analyzing the results of virtual screening (VS) performed with Autodock Vina [1] can be challenging when done manually. In earlier instances, we supplied two scripts, namely vs_analysis.py [2,3] and vs_analysis_compounds.py [4]. This time, we have developed a new Python script to simplify the analysis of VS results.

(more…)

Continue Reading

Software

How to install Interactive Genome Viewer (IGV) & tools on Ubuntu?

Dr. Muniba Faiza

Published

on

How to install Interactive Genome Viewer (IGV) & tools on Ubuntu?

Interactive Genome Viewer (IGV) is an interactive tool to visualize genomic data [1]. In this article, we are installing IGV and tools on Ubuntu desktop.

(more…)

Continue Reading

MD Simulation

[Tutorial] Installing VIAMD on Ubuntu (Linux).

Dr. Muniba Faiza

Published

on

[Tutorial] Installing VIAMD on Ubuntu (Linux).

Visual Interactive Analysis of Molecular Dynamics (VIAMD) is a tool that allows the interactive analysis of molecular dynamics simulations [1]. In this article, we are installing it on Ubuntu (Linux).

(more…)

Continue Reading

Docking

[Tutorial] Performing docking using DockingPie plugin in PyMOL.

Dr. Muniba Faiza

Published

on

[Tutorial] Performing docking using DockingPie plugin in PyMOL.

DockingPie [1] is a PyMOL plugin to perform computational docking within PyMOL [2]. In this article, we will perform simple docking using DockingPie1.2.

(more…)

Continue Reading

Docking

How to install the DockingPie plugin on PyMOL?

Dr. Muniba Faiza

Published

on

How to install DockingPie plugin on PyMOL?

DockingPie [1] is a plugin of PyMOL [2] made to fulfill the purpose of docking within the PyMOL interface. This plugin will allow you to dock using four different algorithms, namely, Vina, RxDock, SMINA, and ADFR. It will also allow you to perform flexible docking. Though the installation procedure is the same for all OSs, in this article, we are installing this plugin on Ubuntu (Linux).

(more…)

Continue Reading

Software

Video Tutorial: Calculating binding pocket volume using PyVol plugin.

Dr. Muniba Faiza

Published

on

Calculate Binding Pocket Volume in Pymol (using PyVol plugin).

This is a video tutorial for calculating binding pocket volume using the PyVol plugin [1] in Pymol [2].

(more…)

Continue Reading

Software

How to generate topology from SMILES for MD Simulation?

Dr. Muniba Faiza

Published

on

How to generate topology from SMILES for MD Simulation?

If you need to generate the topology of molecules using their SMILES, a simple Python script is available.

(more…)

Continue Reading

Software

[Tutorial] Installing jdock on Ubuntu (Linux).

Dr. Muniba Faiza

Published

on

[Tutorial] Installing jdock on Ubuntu (Linux).

jdock is an extended version of idock [1]. It has the same features as the idock along with some bug fixes. However, the binary name and the GitHub repository names are changed. We are installing jdock on Ubuntu (Linux).

(more…)

Continue Reading

Software

How to install GMXPBSA on Ubuntu (Linux)?

Dr. Muniba Faiza

Published

on

How to install GMXPBSA on Ubuntu (Linux)?

GMXPBSA is a tool to calculate binding free energy [1]. It is compatible with Gromacs version 4.5 and later. In this article, we will install GMXPBSA version 2.1.2 on Ubuntu (Linux).

(more…)

Continue Reading

Docking

[Tutorial] Installing Pyrx on Windows.

Dr. Muniba Faiza

Published

on

[Tutorial] Installing Pyrx on Windows.

Pyrx [1] is another virtual screening software that also offers to perform docking using Autodock Vina. In this article, we will install Pyrx on Windows. (more…)

Continue Reading

MD Simulation

How to solve ‘Could NOT find CUDA: Found unsuitable version “10.1”‘ error during GROMACS installation?

Dr. Muniba Faiza

Published

on

How to solve ‘Could NOT find CUDA: Found unsuitable version “10.1”‘ error during GROMACS installation?

Compiling GROMACS [1] with GPU can be trivial. Previously, we have provided a few articles on the same. In this article, we will solve an error frequently occurring during GROMACS installation.

(more…)

Continue Reading

Software

Installing Autodock4 on MacOS.

Dr. Muniba Faiza

Published

on

Installing Autodock4 on MacOS

Previously, we installed the Autodock suite [1] on Ubuntu. Visit this article for details. Now, let’s install it on MacOS.

(more…)

Continue Reading

Docking

How to install Autodock4 on Ubuntu?

Dr. Muniba Faiza

Published

on

How to install Autodock4 on Ubuntu?

Autodock suite is used for docking small molecules [1]. Recently, Autodock-GPU [2] is developed to accelerate the docking process. Its installation is described in this article. In this tutorial, we will install Autodock 4.2.6 on Ubuntu.

(more…)

Continue Reading

Software

DS Visualizer: Uses & Applications

Dr. Muniba Faiza

Published

on

DS Visualizer: Uses & Applications

Discovery Studio (DS) Visualizer (from BIOVIA) is a visualization tool for viewing, sharing, and analyzing proteins [1]. Here are some uses and applications of DS Visualizer.

(more…)

Continue Reading

Software

Protein structure & folding information exploited from remote homologs.

Dr. Muniba Faiza

Published

on

protein structure & folding prediction using remote homologs

Remote homologs are similar protein structures that share similar functions, but there is no easily detectable sequence similarity in them. A new study has revealed that the protein folding information can be exploited from remote homologous structures. A new tool is developed to recognize such proteins and predict their structure and folding pathway. (more…)

Continue Reading

LATEST ISSUE

ADVERT