Based on the description from your lens, it appears your lens has what is known as FTM or full time manual focus. In an automatic focus lens, there has to be a link between a motor and the focus element. In cheaper lenses, the connection is left all the time and trying to manually turn the ring while in auto focus can and will damage the gears or the motor that drives the auto focus. The A/M switch (on the lens) manually disconnects the auto-focus motor.
In more expensive lenses, the motor disconnects from the focus elements when not making adjustments and thus you can make manual adjustments any time that the motor is not trying to make adjustments. I don't know what it is called on Nikon bodies, but on Canon bodies, you want to make sure that you are in One Shot focus mode (where the camera only adjusts the focus once and doesn't try to follow the target). On your camera body, it appears to be the AF-S auto focus mode. If you use a mode that tries to follow the target, the motor will constantly be fighting your attempts to manually focus and damage may occur.
Simply flipping the switch on the lens to M should inform the camera body that you do not wish to use automatic focus and even if the body tried to make adjustments from it's own switch, the lens would simply ignore them since the motor is disengaged from the focus element. In the event that it is an older screw-drive type lens that is driven by the camera body, then the switch on the camera body itself would tell the camera not to try driving the motor mechanically, but on a lens with the motor in the lens, I would guess it wouldn't do anything. (I'm a Canon guy, so hopefully one of the Nikon guys can confirm this.)
Personally, I love full time manual lenses and almost never put them in manual focus mode. There isn't really any reason to do so when you can get the best of both worlds. The only reason I can see to do so would be if you were unable to easily switch the AF mode to not try following focus (on my camera, it's only a button press and a wheel turn away.)
In short, it sounds like with your lens, using the camera on AF, the AF-mode set to AF-S and the lens set to A, you should be able to half depress the shutter and then make manual adjustments to the focus just fine.