I am very new in the field of molecular dynamics and simulation. I want to run MD simulation of protein ligand complex in bound and non bound form. I am learning GROMACS for the same. Can anyone describe the steps involved in such simulation studies. What kind of system is required for such analysis if my protein is 500 amino acid long. Looking forward for your valuable suggestions.
Prof Justin A. Lemkul, has tutorial for GROMACS with special scripts that you will need. it is good for initiate your MD study http://www.mdtutorials.com/
One of the best tutorials ever for a conventional MD simulation using GROMACS is LYSOZYME IN WATER (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html).
A video lecture based on this tutorial is available at https://www.youtube.com/watch?v=rYZ1p5lXNyc
Thanks for your valuable suggestions. I am going through the tutorial. Can anyone tell me, if I have a protein ligand complex. Do I need to make topology file of ligand and protein separately always. In tutorial protein and ligand is prepared separately.
This tutorial may be useful for you.
http://gaznevada.iq.usp.br/wp-content/uploads/gromacs_tutor.pdf
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