Common mistakes made during Autodock Vina Installation and Execution

Several errors occur while installing MGLTools and Autodock Vina on Ubuntu. We have explained the complete process of Autodock Vina installation and docking in previous articles. Here are some common errors and mistakes that should be taken care of while installing and running Vina on Ubuntu.

Errors and mistakes during installation

1. Instruction set on your system

You should always check for the instruction set on your system before you download MGLTools. You can check it by typing the following commands in a terminal:

$ uname -a

$ uname -r

These commands will show you the instruction set of your system. The output should look like this:

$ Linux admin 5.4.0-26-generic #a30-Ubuntu SMP Wed Aug 5 10:58:30 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

Download the MGLTools according to your instruction set, otherwise, it may give you several errors such as:

ImportError: No module named _md5
TclError: couldn’t load file “/home/pc/Downloads/mgltools_i86Linux2_1.5.6/MGLToolsPckgs/opengltk/OpenGL/Tk/Togl/togl.so”: libXmu.so.6: cannot open shared object file: No such file or directory
hit enter to continue

2. Ignore minute errors

Do not ignore minute errors that occur during the compilation of the packages. If the program is not compiled properly then it will not get installed.

3.Creating aliases

While you are creating aliases, don’t forget to check your instruction set in the command and the correct path. The path should consist of the directory where you have installed MGLTools. If you have installed in Downloads, then it should be /home/user/Downloads/mgltools_xxx/bin/adt.

Errors and mistakes while running Vina

1. File location

It is better to keep all files of receptors and ligands in the same directory otherwise you get errors like:

Could not open “protein.pdbqt” for reading
Could not open “ligands.txt” for reading
Could not open “conf.txt” for reading

If you have files in other directories then provide a full path to them. Also, while you are docking in Windows, don’t run Vina command from C:\ drive, you may encounter the above errors due to permission issues.

2. File extension

When you create a file in Windows, try to use Notepad++ and be careful while you are saving configuration or ligands or receptor files. Sometimes, it is possible that you get the same errors as mentioned in point 1. Therefore, when you are saving files, always remember either to set the ‘File type’ as ‘All files’ and type the full filename with an extension (ligands.txt/config.txt) or set the ‘File type’ as ‘text’ and type the only name of the file without any extension (ligands/config. etc.). Otherwise, your filename will become ligands.txt.txt that will not be recognized by the program, and ultimately you will get the error.

3. Configuration File

Be careful while entering coordinates of the binding pocket in config file. If you are performing virtual screening of ligands then neither their names will be entered in the config file nor the ‘ligand’ parameter. In that case, ligand names will be saved in a different file.

4. Ligand file for virtual screening

The naming of ligands for virtual screening depends on the script you are going to use whether Perl or Bash script. it is explained in one of the previous articles.

5. Not enough memory

Make sure you have enough free space available in your disk for Vina installation and execution. If not, then try to allocate some space and then install or execute Vina.

These are the basic things that you should keep in mind before the installation and execution of Autodock Vina on Ubuntu.

Following are some related articles on installation and docking using Autodock Vina:

Here you can find some FAQs for such errors. If you have any such issues, then you can browse some existing questions here or feel free to post questions here.