Are you using any of the 1x slots with cards already?
Why not switch to onboard graphics run by the cpu?
.
.
it's new rig
the rig was working fine with the primary gpu in riser connected to the 16x slot
windows installed well and every thing was going fine
untill i attatched the rest of the cards
then when powring on the rig
every thing got silent
no response at all
no fans rotating not cards lighting nothing at all
then i discovered this melted slot
The answer to your question is yes, you can run the PC without the 16x slot, but that statement assumes nothing else is wrong with the motherboard.
Now that you have indicated the main 16x slot has melted, there may be other component failures and/or short circuits somewhere that would keep the motherboard from posting. Best thing is maybe just to try and RMA the board as you could risk frying your GPU's and other components (CPU, RAM, PSU) if indeed the motherboard is shorted.