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On some motherboards, the first X16 slot may be located too close to the cpu and a cooler may impact the graphics card.
I do not think that is the case with your motherboard.
Here is a chart from noctua as to which coolers can fit:
https://ncc.noctua.at/motherboards/model/ASUS-ROG-Strix B450-F Gaming-4167
Virtually all will fit.

Show a photo of the problem you are having.

Read your motherboard manual.
I suspect that it will say that a card inserted in the second x16 slot will operate pcie 2.0 at X4.
But, possibly at x8 if nothing is in the first slot.
No harm will come if you simply try it.
The question is how much performance loss, if any will you see.
I would expect to see some.
Hi, i just got a new gpu (GTX 1080) and it didn't fit in the first slot, so according to my motherboard it has 2 PCI-E 3.0 x16, i was wondering if ill be fine using the second PCI slot and not lose any performance

This is the motherboard im using: Asus B450-F Gaming (https://rog.asus.com/motherboards/rog-strix/rog-strix-b450-f-gaming-model/)

Thanks!
I'm also confused why you can't fit the 1st slot, but it may be driven by case or CPU cooler interfence.

You can certainly plug your GPU in the 2nd GPU slot and it should boot up with it and operation. But it will probably operate at x8 mode, or maybe even x4 mode, instead of x16 mode so be alert for that.

Check operation with GPUz, click on the little question mark to open a rendering window and see the true PCIe generation and bandwidth since many cards will reduce when they can to lower power consumption.
 
I'm also confused why you can't fit the 1st slot, but it may be driven by case or CPU cooler interfence.

You can certainly plug your GPU in the 2nd GPU slot and it should boot up with it and operation. But it will probably operate at x8 mode, or maybe even x4 mode, instead of x16 mode so be alert for that.

Check operation with GPUz, click on the little question mark to open a rendering window and see the true PCIe generation and bandwidth since many cards will reduce when they can to lower power consumption.
I dont think that there can be a cooler that restricts access to the first pcie slot.
Are there coolers like that?
 
I dont think that there can be a cooler that restricts access to the first pcie slot.
Are there coolers like that?
I can only imagine some strange mounting arrangement...like mounting a large cooler in north/south arrangement where the fan is now located where the GPU would be. I had a cooler with pre-AM4 mounting brackets that forced a mount in that orientation.
 
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On some motherboards, the first X16 slot may be located too close to the cpu and a cooler may impact the graphics card.
I do not think that is the case with your motherboard.
Here is a chart from noctua as to which coolers can fit:
https://ncc.noctua.at/motherboards/model/ASUS-ROG-Strix B450-F Gaming-4167
Virtually all will fit.

Show a photo of the problem you are having.

Read your motherboard manual.
I suspect that it will say that a card inserted in the second x16 slot will operate pcie 2.0 at X4.
But, possibly at x8 if nothing is in the first slot.
No harm will come if you simply try it.
The question is how much performance loss, if any will you see.
I would expect to see some.
 
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