There is no intrinsic limit on the size of the systems that MSMs, or MSMBuilder, can handle. With that said, there may be some significant challenges with a relatively large ternary complex. Chiefly getting enough MD sampling to accurately sample the dynamics. From an MSM perspective, clustering may be challenging and perhaps if the structure is very lrge, there might be some challenges getting all of the information to fit into RAM at the same time. There's no reason that this is not possible, but there could be some challenges. I would recommend you look in the literature at the largest systems that others have studied using MSMs, and the methods they used.
There is no intrinsic limit on the size of the systems that MSMs, or MSMBuilder, can handle. With that said, there may be some significant challenges with a relatively large ternary complex. Chiefly getting enough MD sampling to accurately sample the dynamics. From an MSM perspective, clustering may be challenging and perhaps if the structure is very lrge, there might be some challenges getting all of the information to fit into RAM at the same time. There's no reason that this is not possible, but there could be some challenges. I would recommend you look in the literature at the largest systems that others have studied using MSMs, and the methods they used.