DEV Community: Abdullah Al Nahid

How to install Gromacs, PyMOL, AutoDock Vina, VMD, MGLTools, Avogadro2, Open Babel in Ubuntu 20.04

Abdullah Al Nahid — Sun, 31 Oct 2021 14:34:52 +0000

One of the most time-consuming and frustrating aspects of computational tasks has always been properly installing software and getting it up and running in no time. In the case of bioinformatics tools, this is notoriously difficult in some cases, particularly in Linux-based operating systems such as Ubuntu, where one-click installer files, unlike Windows, are not an option. Although much of the popular software in the bioinformatics world is easy to install in Ubuntu if one is familiar with the ecosystem, a beginner will certainly have a difficult time circling the internet trying to find a proper installation method, at least, that’s what I had to go through when I first started out.

Here in this article, I compiled out the installation methods of some of the most commonly used bioinformatics and simulation tools, as well as how to run these tools after installing them on an Ubuntu 20.04 machine. Feel free to let me know which software should be added next.

Before running any of the commands below, run this command once:

sudo apt-get -y update

1. Avogadro2

Installation

sudo apt-get install -y avogadro

How to run `Avogadro2`

avogadro2

2. PyMOL

Installation

sudo apt-get install -y pymol

How to run `pymol`

pymol

3. Gromacs

Installation

sudo apt-get install -y gromacs

How to run `Gromacs`

gmx

4. VMD

Installation

cd ~

curl -k https://www.ks.uiuc.edu/Research/vmd/vmd-1.9.3/files/final/vmd-1.9.3.bin.LINUXAMD64-CUDA8-OptiX4-OSPRay111p1.opengl.tar.gz --output vmd.tar.gz

mkdir -p vmd

tar -xvzf vmd.tar.gz -C vmd --strip-components=1

cd vmd

./configure

cd src

sudo make install

How to run `VMD`

vmd

5. AutoDock Vina

Installation

sudo apt-get install -y autodock-vina

How to run `AutoDock Vina`

vina

6. MGLTools

Installation

cd ~

curl -k https://ccsb.scripps.edu/download/532/ --output mgltools.tar.gz

mkdir -p mgltools

tar -xvzf mgltools.tar.gz -C mgltools --strip-components=1

cd mgltools

bash install.sh

source ./initMGLtools.sh

How to run `Python Molecule Viewer (PMV)`

pmv

How to run `AutoDockTools (ADT)`

adt

How to run `Vision`

vision

7. Open Babel Command Line Program

Installation

sudo apt-get install -y openbabel

How to run `openbabel`

obabel

8. Open Babel Graphical User Interface (GUI)

Installation

sudo apt-get install -y openbabel-gui

How to run `openbabel gui`

obgui

Linux commands to compress and decompress files and directories

Abdullah Al Nahid — Tue, 14 Sep 2021 09:25:12 +0000

Being an avid linux os user, I often find myself googling how to compress a single file or a directory using bash terminal. The purpose of this article is to compile all those handy commands that I have to copy-paste from internet.

Comment if you want more compression related commands that you frequently use

1A. Compress to tar.gz

###### For a file
tar -cvzf <output-file> <input-file>

###### For a folder
tar -cvzf <output-file> <input-folder>

For example:

###### For a file
tar -cvzf file.tar.gz myfile.csv

###### For a folder
tar -cvzf documents.tar.gz Documents

1B. Decompress tar.gz

tar -xvzf <tar-gz-file>

For example:

tar -xvzf work.tar.gz

2A. Compress to .tar

###### For a file
tar -cvf <output-file> <input-file>

###### For a folder
tar -cvf <output-file> <input-folder>

For example:

###### For a file
tar -cvf file.tar myfile.csv

###### For a folder
tar -cvf documents.tar Documents

2B. Decompress .tar

tar -xvf <tar-file>

For example:

tar -xvf work.tar

3A. Compress to .gz

gzip <filename>

###### To keep the original input file:
gzip -k <filename>

For example:

gzip documents.txt

###### To keep the original input file
gzip -k documents.txt

3B. Decompress .gz

gunzip <gz-file>

###### To keep the original compressed file:
gunzip -k <gz-file>

For example:

gunzip filename.gz

###### To keep the original compressed file
gunzip -k filename.gz

4A. Compress to .zip

###### For a single file
zip <output-zip-file> <input-filename>

###### For multiple files
zip <output-zip-file> <file-1> <file-2> ... <file-n>

###### For multiple files with same extension (.csv, .pdf) 
zip <output-zip-file> *<extension>

###### For a folder
zip -r <output-zip-file> <input-folder-name>

###### For multiple folders
zip -r <output-zip-file> <folder-1> <folder-2> ... <folder-n>

For example:

###### For myfile.txt file
zip document.zip myfile.txt

###### For multiple files
zip files.zip report.docx document.pdf data.txt

###### For multiple files with same extension (.csv, .pdf)
zip pdfs.zip *.pdf
zip textfiles.zip *.txt

###### For Documents folder
zip -r temp.zip Documents

###### For Books and Documents folders
zip -r folders.zip Books Documents

4B. Decompress .zip

unzip <zip-filename>

For example:

unzip document.zip

In case of error unzip command not found, run this:

sudo apt-get install unzip

Bash Commands for Bioinformatics Beginners: Part 1

Abdullah Al Nahid — Sat, 26 Sep 2020 16:07:15 +0000

Disclaimer: This article is a collection of useful bash commands that I have been using regularly.

1. Count Fasta Sequences

This command will help you to count fasta sequences in a fasta file.

grep -c ">" <fasta-file-name>

Example: grep -c ">" sequences.fasta

2. Count Empty Lines

If you want to count empty/blank lines in a file, then this command will help you.

grep -c "^$" <file-name>

Example: grep -c "^$" sequences.fasta

3. Remove Empty Lines

To remove empty/blank lines from a file, this command is useful.

sed -i "/^$/d" <file-name>

Example: sed -i "/^$/d" sequences.fasta

4. Merge Multiple CSV Files

If you have multiple CSV files with same header, then you can use this command to merge them. The command below has two parts.
In the head -n 1 <a-csv-file> > combined.out part, replace <a-csv-file> with any of the .csv file. Check example section for better understanding.

head -n 1 <a-csv-file> > combined.out && tail -n+2 -q *.csv >> combined.out

After running this command, rename the combined.out file to combined.csv

Example:
Suppose, you have 4 csv files.
file1.csv
file2.csv
file3.csv
file4.csv
So your should run:
head -n 1 file1.csv > combined.out && tail -n+2 -q *.csv >> combined.out
Then you will see a new combined.out file. Don't forget to rename this file to combined.csv

5. Unzip all zip files

Unzipping all .zip files in a folder is a breeze with this command.

unzip "*.zip"

However, this command will not delete the .zip files after unzipping. If you are looking for a command to delete all the files with same file format (.zip, .gz, .txt), then scroll below.

6. Delete all files with same file format

Suppose, you want to delete multiple files with same file format, then these two commands will come in handy for you.
First, check what files you are going to remove:

find . -name "*<file-type>" -type f

Then, run the delete command:

find . -name "*<file-type>" -type f -delete

Check the example part for better understanding.

Example:
If you want to delete all the .gz files, then the commands should look like this:

find . -name "*.gz" -type f
find . -name "*.gz" -type f -delete

To delete all .zip files:

find . -name "*.zip" -type f
find . -name "*.zip" -type f -delete

That's all for now. Feel free to add more bash commands in the comments section and I will add them to the article.

DEV Community: Abdullah Al Nahid

How to install Gromacs, PyMOL, AutoDock Vina, VMD, MGLTools, Avogadro2, Open Babel in Ubuntu 20.04

Before running any of the commands below, run this command once:

1. Avogadro2

Installation

How to run Avogadro2

2. PyMOL

Installation

How to run pymol

3. Gromacs

Installation

How to run Gromacs

4. VMD

Installation

How to run VMD

5. AutoDock Vina

Installation

How to run AutoDock Vina

6. MGLTools

Installation

How to run Python Molecule Viewer (PMV)

How to run AutoDockTools (ADT)

How to run Vision

7. Open Babel Command Line Program

Installation

How to run openbabel

8. Open Babel Graphical User Interface (GUI)

Installation

How to run openbabel gui

Linux commands to compress and decompress files and directories

1A. Compress to tar.gz

1B. Decompress tar.gz

2A. Compress to .tar

2B. Decompress .tar

3A. Compress to .gz

3B. Decompress .gz

4A. Compress to .zip

4B. Decompress .zip

Bash Commands for Bioinformatics Beginners: Part 1

1. Count Fasta Sequences

2. Count Empty Lines

3. Remove Empty Lines

4. Merge Multiple CSV Files

5. Unzip all zip files

6. Delete all files with same file format

How to run `Avogadro2`

How to run `pymol`

How to run `Gromacs`

How to run `VMD`

How to run `AutoDock Vina`

How to run `Python Molecule Viewer (PMV)`

How to run `AutoDockTools (ADT)`

How to run `Vision`

How to run `openbabel`

How to run `openbabel gui`