I am interested in Molecular dynamics calculation. After finishing the docking, I would like to carry out dynamics calculation to understand the stability of the ligand-protein pose. If anyone can help me I would be grateful.
Please suggest me some good tutorial, books, articles or manuals etc.
See if this could be of some help.
I have done MD Simulation by this only.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
The easiest way would be to use Schrodinger maestro. The academic version is free and you can obtain it from: http://www.deshawresearch.com/downloads/download_desmond.cgi/. And there are a lot of tutorials too (https://www.schrodinger.com/training/tutorials). I would suggest desmond because it will also generate a whole lot of analysis on the MD by only a single click (https://www.schrodinger.com/newsletters/introducing-sid-simulation-interactions-diagram).
Alternatively, you may go for gromacs, which is widely used. There are some good tutorials too (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html). It is not for the beginners, though.
I strongly recommend you to study at lest one book about molecular modeling approaches before carrying out any test.
https://www.amazon.com/Molecular-Modelling-Principles-Applications-2nd/dp/0582382106
See if this could be of some help.
I have done MD Simulation by this only.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
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