Opening a MOL2 File

The MOL2 file type is primarily associated with SYBYL.

MOL2	File extension: MOL2
	File type:	molecule data file

What is a MOL2 file

MOL2 files mostly belong to SYBYL by Certara. Tripos MOL2 is a free format ASCII file that acts as a portable representation of a molecule used in the fields of cheminformatics and bioinformatics. It originated in the expert molecular modeling environment SYBYL created by Tripos. The contents of these files are interpreted as code that contains information about molecules by specialized software environments.

Structure: The content structure includes comments and blank lines as well as sections known as 'Record Type indicators' and 'Data Records'. There are 32 different possible formats of a data record, depending on the section of the file in which the data record resides. These are all referenced in the official documentation available for free.
Associated programs: There is a plethora of free solutions which can be used to read, create, and convert MOL2 files. Some of these solutions include ICM Browser by Molsoft, Open Babel, and Wolfram.

How to open a MOL2 file

You need a suitable software like SYBYL to open a MOL2 file. Without proper software you will receive a Windows message "How do you want to open this file?" or "Windows cannot open this file" or a similar Mac/iPhone/Android alert. If you cannot open your MOL2 file correctly, try to right-click or long-press the file. Then click "Open with" and choose an application. You can also display a MOL2 file directly in the browser:. Just drag the file onto this browser window and drop it.

Online MOL2 Text Viewer

Choose your .mol2 file to view

or drag and drop it here

Online File Viewer

✈

Read our privacy guarantee in Filext’s terms and privacy policy

Please allow ads on our site

This helps us keep our servers running. Then re-upload your file to view it.

Click here to see how to disable the ad blocker for filext.com

How to extract texts from MOL2 files or capture a screenshot to PDF, JPG, DOCX, TXT, ...

If you want to extract texts from MOL2 file or capture a screenshot, you can use our free Online MOL2 File Viewer:

To do this, click the button "Choose your .mol2 file to view" on this page.
Your MOL2 file will then be displayed in the browser.
Now click on "Save as..." at the top of the page.
Then choose the file format (e.g. JPG, PDF, DOCX, TXT, ...) you want.
Download the converted file.

Programs that open and convert MOL2 files:

SYBYL by Certara
See the previous paragraphs to learn more about the main application. MOL2 files are often referred to as SYBYL simple text files because this type of file is primarily created or used by this software.
WebLab Molecular (viewer file) by Molecular Simulations
WebLab is a free molecular viewing software that can represent alpha helices as cylinders, add missing hydrogen atoms, and rotate residues around a bond. This program is primarily designed to run on Windows and Mac OS systems, however, has the capabilities of running on Linux as well. The MOL2 file contains the viewing file as well as the molecular information for each individual molecule. This file format is classified as Data. Related links: Free molecular modeling software, https://www.york.ac.uk/org/seg/salters/ChemistryArchive/download.html

MOL2 format details:

Each file has a definite file format, that is, how the stored data is arranged in the file. A file format is determined by the file extension and signature, so JPEG images have the extension .jpg and the first bytes in the file are ÿØÿ. If the file extension does not match the file format, double-clicking on the file will cause an error upon opening. When there is a problem with a file, the first step to solving it is to determine the file format. Below is our analysis of the MOL2 files:

MOL2 is seldom used as a file extension and includes different formats for the applicable programs. The two most popular formats are as follows:

60% of all MOL2 files use the same file format, which have the signature @<TRIPOS>MOLECULE. These files are text files, so they contain words and text. A typical file size is 8 KB. The file type was developed only in the last few years. The following keywords are characteristic: @<TRIPOS>ATOM, @<TRIPOS>MOLECULE, SMALL and USER_CHARGES. Such files sometimes refer to ligand.
30% of all MOL2 files belong to Tripos Mol2. These files contain text and words, not binary data. MOL2 files can be up to 80 MB in size, but are often around 2 KB - 50 KB. The following keywords are characteristic: Name, @<TRIPOS>MOLECULE, SMALL, CHARGES, Created, USER, @<TRIPOS>ATOM and Creation time.

All other MOL2 files (10%) have no consistent format. Just click the "Choose your .mol2 file to view" button on this page to find out what your MOL2 file is.

Technical Data for MOL2 File Extension

File classification:

Simple text file

Related files:

mol, pdb, cml, gz, zip, txt, jpg, xsr, mph

Mime type:

chemical/x-mol2

a mol2 molecule data file is a special file format by Certara and should only be edited and saved with the appropriate software.

How to solve problems with MOL2 files

Associate the MOL2 file extension with the correct application.
Update your software that should actually open molecule data files. Because only the current version supports the latest MOL2 file format. Search, therefore, e.g. on the Certara manufacturer website after an available SYBYL update.
To make sure that your MOL2 file is not corrupted or virus-infected, get the file again and scan it with Google's virustotal.com.
Click here to open your .MOL2 file online - secure, fast, and no downloads needed.