Small ship to big ship can be done with sphere to triangle-mesh collision. At least my nxPascal can calculate nearest point on a model and a normal at that point. You may use the information for collision.
Big ship to big ship might need triangle to triangle collision, which might be much harder to implement, and slower.
edit: Actually vertex to triangle would be enough in most cases. Just don't have the polygons so big that ship section could pass through them.
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