Could anyone tell me the step by step procedure to perform MD simulation of protein-ligand complex using the BRAF server ?

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Shaban Ahmad

https://www.researchgate.net/post/Is_anyone_using_BRAF_facility_of_C-DAC_Pune_for_MD_with_Gromacs

Anuj Kumar

Gajula et al. 2016. Protocol for Molecular Dynamics Simulations of Proteins (https://bio-protocol.org/e2051).

Muhammad Aqib Shabbir

This tutorial may be h elpful for you

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html