In Ubuntu there's nothing to install actually. You have to unzip it and that's it. Then you have to run it from the terminal using the command:

java -cp [path] -jar [path]LigPlus.jar

where the [path] is the path to the directory where the LigPlus.jar file is located.

But for the first time you must run it with a sudo command i.e., sudo java -cp... or in a root terminal.

For more clarity follow the steps here:

1. Unzip the downloaded file. From the right click menu choose extract here.

2. Name the folder as "LigPlus" if it is not already named so.

3. Cut the folder and paste it inside the folder /usr/bin/

4. Open a terminal and type "sudo java -cp /usr/bin/LigPlus/ -jar /usr/bin/LigPlus/LigPlus.jar" use "sudo" only for the first time.

5. when asked give your administrative password.

6. Enjoy LigPlus.

In Ubuntu there's nothing to install actually. You have to unzip it and that's it. Then you have to run it from the terminal using the command:

java -cp [path] -jar [path]LigPlus.jar

where the [path] is the path to the directory where the LigPlus.jar file is located.

But for the first time you must run it with a sudo command i.e., sudo java -cp... or in a root terminal.

For more clarity follow the steps here:

1. Unzip the downloaded file. From the right click menu choose extract here.

2. Name the folder as "LigPlus" if it is not already named so.

3. Cut the folder and paste it inside the folder /usr/bin/

4. Open a terminal and type "sudo java -cp /usr/bin/LigPlus/ -jar /usr/bin/LigPlus/LigPlus.jar" use "sudo" only for the first time.

5. when asked give your administrative password.

6. Enjoy LigPlus.

If you have followed the steps above and are able to run LigPlus, you may now create a desktop entry to make the life a lot more easier. Copy and paste the following content in a text file:

#!/usr/bin/env xdg-open

[Desktop Entry]

Version=1.4

Name=LigPlot+

Exec=java -cp /usr/bin/LigPlus/ -jar /usr/bin/LigPlus/LigPlus.jar %f

Icon=/usr/share/icons/ligplus.gif

Terminal=false

Type=Application

Categories=Java;Science;Chemistry;Physics;Education;

StartupNotify=true

Open the text editor and copy the information above and save it as "LigPlus.desktop". You may put the file anywhere. You can now launch LigPlus just by double clicking the file. If you want it to appear in Dash application list and Dash search you have to copy the file into the following directory

/usr/share/applications/

LigPlot+ will now appear on Dash search and in the installed application list in Application lens.

Dear All,

I tried to install LigPlus in Ubuntu 14.04 following the six steps mentioned in above. But when I run the LigPlus (I tried to identify the interactions between EVP molecule in pdb 3QX3) it gives an error as follows. Can anyone help me to sove this problem. I gave the pathways according to the attached screenshot.

The error I obtained is,

amali@amali-OptiPlex-7010:~$ sudo java -cp /usr/bin/LigPlus/ -jar /usr/bin/LigPlus/LigPlus.jar

[sudo] password for amali:

In inits ... Font family = null

Operating system = linux

EXE directory = lib/exe_linux

Location = /usr/bin/LigPlus/LigPlus.jar

2. Found library directory at /usr/bin/LigPlus/lib

2. Found exe directory at /usr/bin/LigPlus/lib/exe_linux

Current directory set to: .

Reading parameter file: /usr/bin/LigPlus/lib/params/defaults.linux

0. Reading parameter file: /usr/bin/LigPlus/lib/params/ligplus.par

1. Reading parameter file: /home/amali/ligplus.par

Setting currentDirectory to null

Image file read in: /usr/bin/LigPlus/lib/images/ligplus_logo.gif

Image file read in: /usr/bin/LigPlus/lib/images/rotate.gif

Image file read in: /usr/bin/LigPlus/lib/images/flip.gif

Icon read in: /usr/bin/LigPlus/lib/images/rasmol_logo.gif

Icon read in: /usr/bin/LigPlus/lib/images/pymol_logo.gif

currentDirectory: null

Saving parameters to: /usr/bin/LigPlus/lib/params/ligplus.par

Open PDB file item selected

Text entered: []

Opening: /home/amali/Desktop/3QX3/3qx3.pdb

File name: 3qx3.pdb

Directory: /home/amali/Desktop/3QX3

Reading .pdb file ...

Reading PDB file: /home/amali/Desktop/3QX3/3qx3.pdb

FOUND METAL: [MG]

FOUND METAL: [MG]

FOUND METAL: [MG]

FOUND METAL: [MG]

FOUND METAL: [MG]

FOUND METAL: [MG]

PDB code: 3qx3

No. of residues read in: 2437

No. of atoms read in: 12783

Interacting molecule pairs:

0. protein chainLYS 452 (A)-ASP 1201 (A) : protein chainSER 449 (B)-ASP 1201 (B)

Selected LIGPLOT ...

Starting background job ...

Done with ok = true

Other event: state

*** Warning: long CONECT record: 11925 MG MG 1223 (A) - 12378 O HOH 1466 (A) Dist = 2.514081

*** Warning: long CONECT record: 12378 O HOH 1466 (A) - 11925 MG MG 1223 (A) Dist = 2.514081

Calling HBADD ...

Running HBADD

Het Group Dictionary: /data/pdbsum/pdbsum/data/components.cif

Temporary PDB file: /tmp/lig8901888969324894501/ligplus.pdb

Command: /usr/bin/LigPlus/lib/exe_linux/hbadd /tmp/lig8901888969324894501/ligplus.pdb /data/pdbsum/pdbsum/data/components.cif -wkdir /tmp/lig8901888969324894501/

java.io.IOException: Cannot run program "/usr/bin/LigPlus/lib/exe_linux/hbadd": error=2, No such file or directory

Other event: state

Thank you.

Hi, i just had the same problem, but i solved it.

The problem is about incompatibilities in the executable for linux. It is for 32 bits, and if you try to run it in a 64 bits system, it will crash

Do this

su dpkg --add-architecture i386 apt-get update apt-get install ia32-libs reboot

I know this question is specific for Ubuntu, but if someone else is looking for the same error in a Fedora box... the solution is to do as root `dnf install glibc.i686`

Thanks to Claudia Mejías Márquez