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.
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:
- How to install AutoDock Vina on Ubuntu?
- Video tutorial: How to install Autodock Vina on Ubuntu?
- How to perform docking in a specific binding site using AutoDock Vina?
- Video Tutorial: How to perform docking using Autodock Vina
- How to perform blind docking using AutoDock Vina?
- How to perform virtual screening using Autodock Vina?
- Site-specific docking: Frequently Asked Questions & answers for starters
Virtual Screening using Autodock Vina: Frequently Asked Questions & Answers for Starters
Virtual Screening (VS) is one of the important techniques in bioinformatics. It can be easily performed using Autodock Vina. We have provided detailed articles on this topic. In this article, we are trying to answer some FAQs for beginners. (more…)
[Tutorial] How to perform docking of zinc metalloproteins using Autodock Vina?
Proteins containing zinc atoms are docked in a different way than that of the normal simple proteins. Zinc atoms must be considered by a force field during the docking process. In this article, we are going to dock zinc metalloprotein with a ligand using Autodock Vina . (more…)