simulation of Gal80

It involves the interaction between all pairs of atoms excluding the bonded atom as it is already involved in bonded term. For weak dipole attraction and repulsion depending upon distance between atoms is accounted by the Lennard-jones potential which is given by:-

2) VMD :- It is a program for molecular visualization, modelling and analysis of biological systems like proteins, nucleic acid, and lipid bilayer assemblies. VMD also gives option to work with volumetric data, sequence data, and arbitrary graphics objects. VMD includes Tcl and Python interpreters, so users can run their own script of these.
VMD is preferred over others program because of its following unique features :-

Can operate on multi-gigabyte molecular dynamic trajectories.
Interoperability with a large number of simulation packages.
Its ability to integrate structure and sequence information.

Other key features are:- Visualization of 3-D molecular with different patterns.
Can display and select subsets of atom from atom selection syntax. Can visualize dynamic molecular and volumetric data.
Major molecular data file formats are supported.
Capability of movie making.
Interactive molecular dynamics simulation.
Source code is written in C and C++.

STEPS IN SIMULATING A PROTEIN:-

STEPS FOLLOWED FOR STIMULATING GAL80 PROTEIN

1) PDB file for Gal80 is downloaded from protein data bank. (PDB id-3V2U)

2) Using modeller, a new 3-d structure from FASTA format of chain A of Gal80 is modeled. This is done because PDB structure has missing atoms from 1-14 and 327-338 .

3) PSF file for modeled Gal80 is generated using automated PSF option of VMD.

4) Minimization of newly modelled 3-D Gal80 structure.

Initial co-ordinate is available from PDB file but it does not correspond to minimum in potential energy. So, minimization is done for:-

Adjustment