Computational Chemistry Facilities

 

 

Hardware:

 

 

Extensive computer facilities are available for the students at the laboratory and have been greatly expanded. The newly updated computer facility contains over twenty desktop (mcg01 to mcg20) computers running a variety of scientific and chemistry related software. SuSE is our main operating system to perform computational chemistry related projects.

 

Additionally a LINUX cluster system has recently been installed to facilitate the long computational chemistry calculations with 10 nodes, each having the Quard Core Xeon T processors of 2.66 GHz

 

 

 

 
 
 
Software:

 

Following Software are in used for research in the laboratory  

 

Molvision is the most flexible tool to visualise chemical systems, from simple molecules to large biopolymers and dynamics of liquids and multi-component solutions.

 

MOE2009  is a comprehensive system that addresses the needs of the variety of research displines. These include: Molecular Modelling and simulation, protein Modeling, bioinformatics, structure based design, High Throughput Discovery, and chemoinformatics.

 

Gaussian View  is used to predicts the energies, molecular structures, and vibrational frequencies of molecular systems, along with numerous molecular properties derived from these basic computation types. Further, it can be used to study molecules and reactions under a wide range of conditions. 

 

AutoDock4.0  is a suite of programs designed to predict the bound conformation(s) of a flexible ligand to a macromolecular target of known structure, like an enzyme or DNA.

 

AutoDockTools 1.4.6 or ADT, can use it to set up, run and analyze AutoDock dockings and isocontour AutoGrid affinity maps, as well as compute molecular surfaces, display secondary structure ribbons, compute hydrogen-bonds, and do many more useful things.

 

FlexX  FlexX is a first, flexible docking method that uses on incremental construction algorithm to place ligand into an active site. It predicts geometry of protein-ligand complex and estimate binding affinity in less than 15 seconds. 

 

Ligplot and LigEd automatically generates schematic diagrams of protein-ligand interactions for a given PDB file. The interactions shown are those mediated by hydrogen bonds and by hydrophobic contacts.

 

VMD1.8.7 (Visual Molecular Dynamics) is a molecular graphics program designed for the interactive visualization and analysis of biopolymers such as proteins, nucleic acids, lipids and membranes.

 

Amber10.0 is a suite of programs that to carry out molecular dynamics (MD) simulations, particularly on biomolecules.

 

Babel 2.1.1 is a popular program to interconvert a number of file formats used in molecular modeling.

 

Molden4.6 is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK , GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac, it also supports a number of other programs via the Molden Format.

 

DOCK 6.0 addresses the problem of "docking" molecules to each other. DOCK algorithm addressed rigid body docking using a geometric matching algorithm to superimpose the ligand onto a negative image of the binding pocket

 

GOLD is a program for calculating the docking modes of small molecules into protein binding sites.

 

DS-viewer is an interactive graphical data structure presentation facility through Discovery Studio (DS) Visualizer. 

   

Free molecular visulization softwares, Protein Explorer.   Rasmol, Pymol, GeneDoc , SPDBV, Procheck TreeView, ClustalX, OMEGA2