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Our VMD Extensions
molUP is a VMD extension that provides a simple manner for loading and saving Gaussian files, and analyze related results. molUP provides a graphical interface for VMD where the users can load and save chemical structures in the Gaussian file formats. This extension includes a set of tools to set up any calculation supported by Gaussian, including ONIOM; analyze energies through interactive plots; animate vibrational frequencies; draw the vectors associated with those frequencies; modify bonds, angles, and dihedrals; and collect bibliographic information on the employed methods.
Visualization can be a motivating way of teaching students about the microscopic world. This can become even more exciting if the information is based on accurate computational results rather than on crude approximations that eventually might create unreal alternative perceptions. Here, we report on a VMD plug-in – VMDMagazine, which can play and handle computational simulations into stunning high-impact video presentations, suitable for classes/lectures and even conferences. The software will help students/audience to understand atoms and molecules better and learn to like them.
VolArea is a plug-in of the widely spread molecular graphics software Visual Molecular Dynamics (VMD), which allows the calculation of the volume as well as the surface area of any chemical structure.The surface area can be used also to map or calculate the exposed area of the structure to the solvent or to another chemical structure. This is particularly useful to characterize protein:ligand complexes or corresponding binding sites, as well as protein:protein interfaces. The volume algorithm can be used to predict the space occupied by any chemical structure as well as that of cavities, such as tunnels, clefts, etc.
Molecular docking is becoming an important part in the process of developing new drugs. There is much docking software that has been successfully used in a myriad of keystone problems, however, as commonly happens with most of the scientific software, the programs are often complex and a deep knowledge is required for the common user to carry out standard steps. This is an obstacle and a cornerstone issue for the research teams in the fields of Chemistry and the Life Sciences, who are interested in conducting this kind of calculations but do not have enough programming skills.
Protein-protein interactions play a crucial role in molecular recognition and cellular function. Mapping them, provides important insight on how these structures interact and on how to improve or inhibit their binding. CompASM presents here as a very intuitive plug-in for two widely distributed softwares ( AMBER-Visual Molecular Dynamics (VMD)) that allows the user to perform a full Alanine Scanning Mutagenesis (ASM) procedure, requiring only very little user effort. This software is composed by two main packages: the Core and Graphical User Interface (GUI).
Chem-Path-Tracker is a bioinformatic tool that allows to locate functionally relevant chemical motifs in protein structures. The chemical motifs can be a small group of residues or structure protein fragments with highly conserved properties that have important biological functions. However, the detection of chemical motifs is rather difficult because they often consist of a set of amino acid residues separated by long, variable regions, and they only come together to form a functional group when the protein is folded into its three dimensional structure. Furthermore, the assemblage of these residues is often dependent on non-covalent interactions among the constituent amino acids that are difficult to detect or visualize. To simplify the analysis of these chemical motifs and give access to a generalized use for all users, we developed Chem-Path-Tracker.
This toolbar allows you to reach easily and faster to all common used command available on VMD. Moreover, this plugin provide an easy to use interface to render beautiful images.
More Details | GitHub Repository
VMD is an exceptional program to visualize molecular structures. The main drawback of this software is the learning curve that turns it hard to use by non-expert users. One of the major difficulties that non-expert users have while handling VMD regards the selection of atoms. This is done through a series of keywords that the user must dominate in order to for example visualize and/or hide particular parts of the molecule, do specific transformations on the atoms of that selectin, etc.
More Details | GitHub Repository
|BioSIM Augmented Reality
Tridimensional structures of molecules are displayed in Augmented Reality (AR) using any device with a camera, browser, and internet connection.
Tcl script to handle Gaussian input and output files. This script allows the extraction of energies and structures.