Molecular Dynamics Simulation

G protein Numbering

This web server allows comparing different Gα protein sequences and structures by mapping them to the Common Gα Numbering system.

link ('A universal allosteric mechanism for Gα protein activation', Tilman Flock , Nature (2015).

General Steps of MD:

1) Acquire PDB of system and remove hydrogen atoms using VMD

2) Build solvated periodic box using CHARMM.gui server

3) Create inpcrd & prmtop files from Charmm output

4) Alternative method is using charmm2amber.py in order to avoid all the renaming of the files

5) MD prep

tleap: Creating an Explicit Protein Waterbox System for Molecular Dynamics (MD) Simulation