There may be some OS and software that might not run on AMD processors. But 99% of all software will run fine.
Some OS doesnt support amd at all they are only available for x86.
Also AMD processors are all x86 compatible. (x86 is just a set of instructions that the processor can perform)
If a software needs x86 or x86-64 it WILL run on AMD. If it needs some other special instructions then it might not. eg. MAC OSX had trouble running on Intel and Amd chips because they used some special instructions available only on IBM sparc processors. But even they moved to x86 compatible code.