Hello,
I'm trying to see the interaction between the Sa Cas9 protein and the guide RNA. I ran a molecular dynamic simulation on it and then estimated the energy binding using the g_MMPBSA command. The issue I have is the values are really really big as you can see. I am wondering if I should adjust some parameters as the dieletric constant? Or maybe the values are correct but high because there is a lot of atoms interacting (the Cas9 contains 1050 AA and the guide RNA is 73 nucleotide long)?
I also add the .mdp file I am currently using.
Thanks a lot
Antoine
Cardiff University
Suparna Ghosh
Hi, please have a look at this package, and give it a try - gmx-MMPBSA.
Link - https://pypi.org/project/gmx-MMPBSA/
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