I am currently working with a multidomain protein: 5 domains in the main body plus a substrate carrier domain protruding from it, covalently attached to the main body by a 40Angstrom linker. I want to simulate the motion of the linker-attached substrate carrier from domain A to domain B (both present in the main body), sampling the most favourable path.
My question is which method can I use to answer this. I have no indication of a specific path, no intermediate coordinates, I only have the structures for the complex Carrier/Domain A (starting point) and Carrier/Domain B (end point). My guess is Meta-dynamics however I don't feel confident as I may lack collective variables good enough to drive such simulation.
Thank you,
Matilde
You can try Targeted Molecular Dynamics (TMD) on NAMD [1]. This procedure applies a restraint in your system during the simulation to guide the initial conformation to your end point. Alternatively, you can apply the CoMD protocol [2], that combines TMD with Anisotropic Network Model (AMD) simulations to perform this kind of simulation.
[1] http://www.ks.uiuc.edu/Research/namd/2.11/ug/node47.html
[2] http://prody.csb.pitt.edu/comd/
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