How to change body velocity with a script?

script.Parent.Touched:Connect(function(V)
	if V.Parent:FindFirstChild("Trian") then
		print("TrainWasFound")
		V.Parent.Main.BodyVelocity.Velocity.X = -5
	end
end)

The positional components of a Vector3 are immutable, meaning that you can't edit the properties directly or it'll return an error. You will have to create a new vector with the new X component:

script.Parent.Touched:Connect(function(V)
	if V.Parent:FindFirstChild("Train") then
		print("TrainWasFound")
		local vel = v.Parent.Main.BodyVelocity.Velocity
		V.Parent.Main.BodyVelocity.Velocity = Vector3.new(-5, vel.Y, vel.Z)
	end
end)

At least try to include some context of the issue you're having, how you intended to behave and any error(s) in your questions