Information Technology and Us

Great Yet Free Computational Chemistry Applications: Avogadro, BKChem, AutoDock, Chimera, MOPAC, Firefly, NWChem and ORCA

Just as some free operating systems such as Ubuntu 16.04 and Lubuntu 18.04, along with their compatible free applications such as LibreOffice and nomacs, provide great computer-work environment comparable in their abilities to costly alternatives such as Windows 10, similarly great yet free computational chemistry programs do exist, competing well with their costly alternatives such as the Gaussian package along with their associated visualization software.

Any computational chemistry investigation (say, the one in this nicely done Master of Science Project under me on computational investigation of a kind of drug-DNA interactions - with its brief slide presentation here) generally starts with preparing (or downloading and refining) the (computer-based) models of the molecular/macromolecular structures. For preparing or refining such models, one needs a molecular editor and visualizer such as Avogadro - this one in particular is a great cross-platform free software (may see this elementary guide booklet by this author, about molecular model preparation in general and about using Avogadro). Avogadro is rather intuitive to learn, yet is aided by this well-written online manual (the manual is best accessed via its left panel). The download size of Avogadro is only in a few tens of MB - it is a graphical software with a simple, direct installation procedure (may of course need administrator privilege!) in both Windows and Linux computers. [In Linux systems, it may be installed through the common graphical package managers such as the default software center and synaptic, etc.]

The molecular model that such a molecular editor makes is essentially (internally) a specification of its constituent atoms along with their positions, these positions being either specified as their nuclear Cartesian (i.e., x, y, z) coordinates (as shown below), or specified in terms of the bond distances, bond angles and dihedral angles - for better details, may read this old webpage of mine. However, to the user the molecular editor presents a colourful 3-D image (as shown below to the right) of the modelled molecule, with facilities to rotate, translate and zoom it. We also found (as seen in the aforesaid project report) Avogadro to be particularly useful in calculating the molecular energy as per the simpler MM (molecular mechanics) theory and thereby to speedily optimize the molecular geometry of the constructed models, using various options of MM force fields, namely UFF, GAFF, MMFF94, MMFF94s and Ghemical.

[To instead learn two-dimensional drawing of chemical structures and reactions, suitable for contributing to chemistry textbooks and research publications, using the simple yet powerful cross-platform freeware BKChem, may go through this elementary guide booklet and this introductory tutorial video on YouTube by this author.

On the other hand, to learn operating the free, user-friendly AutoDock and AutoDock Vina packages for molecular docking (i.e., theoretically checking the possible combinations) of various drug candidate molecules into a bio-macromolecule receptor (aided by the graphical AutoDockTools (ADT) and Python Molecular Viewer (PMV) packages as per the renowned 2012 ADT Tutorial by Huey, Morris and Forli), and to visualise the docking results using PyMOL, Discovery Studio Visualizer and PLIP, may go through this Elementary Guidebook by this author. Here is a fine Master of Science Project under me on molecular docking using these two software, with its short slide presentation here.]

Chimera (UCSF Chimera) is not exactly a molecular editor, but a valuable tool for visualization and analysis of molecular structures and related data such as density maps. In my case, I found it to be particularly useful for visually combining two molecular structures into a combined one in any desired orientation, as explained in the aforesaid project report and also in this older, equally elegant Bachelor of Science Project. Chimera is also useful for appropriately adding (using the AddH plugin) the missing hydrogen atoms in molecular or macromolecular structures obtained from experimental diffraction studies.

Installation of Chimera in Windows is easy - just need to run the installer executable file (from an administrator account). Installation in Linux systems involve running the downloaded executable (generally named chimera-installer.bin, size around 150 MB) in a terminal window (common shortcut Ctrl+Alt+T) with directory changed to the folder containing the downloaded file (say by entering cd Downloads - note that in Linux, the alphabet case is important - i.e., cd downloads doesn't mean the same). Type and enter ls (means, 'list the files and folders here') to see if the said .bin file is seen there, then enter chmod +x chimera-installer.bin to make it executable, then run ./chimera-installer.bin (or, better, sudo ./chimera-installer.bin) to finally install it. The beginning part './' here means 'in this very folder' (in my Lubuntu 18.04 system, without this prefix the installer didn't run) whereas 'sudo' means 'superuser do', i.e., 'working as the administrator' (requires typing the password upon asked). After the installer runs, the UCSF Chimera icon is found on the desktop screen and from the prominent applications launcher by typing in a few starting letters, which may then be double-clicked.

Chimera Visualising a Drug Model

Chimera Combining Base Models

MOPAC (having the moderately detailed online manual) allows, through a (non-graphical) command-line process (using the command prompt in Windows or terminal in Linux), quantum chemical computations of the less accurate but faster semi-empirical kind, as per the methods MNDO, AM1, PM3, PM6, RM1, MNDO-d and PM7. The download size is small (~ 7-8 MB), but licenses are free only for researchers in academic institutions, with an academic-institutional email account being a must; need to apply to the organisation via an online form, in reply to which a password and the (moderately complicated) installation instructions are sent back.