[Chimera-users] Setting a pathway/trajectory for a molecule

[Rani Wiswedel]

Good day,

I am an honours student attempting to set up my first molecular dynamics simulation, and am having some trouble trying to understand how to set a pathway for a substrate through a pore in Chimera. I am very unsure of how to do this, and was wondering if you could provide some help. I tried following the Trajectory and Ensemble Analysis tutorial, but essentially cannot get past the first step of downloading leap.top etc. I am also not sure if this is the correct tutorial to follow for what I am looking to do?

Any advice would be greatly appreciated, I am in way over my depth.

Thank you

Kind regards,
Rani

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