the documentation says that cisTEM is optimized to run on Intel processors. Will the program run on an AMD rig but with non-optimal performance compared to a comparable Intel processor? or will we need to do extensive modification of libraries, etc. to get it to run in the first place?
You won't need to change any of the code to get it to run. It is possible the supplied binaries will not run, or if they do run they won't be optimal on an AMD system, so I would definitely compare the speed to a version compiled with GDB. It should be pretty easy to compile, if you have any problems post on the forum and we can help you out.
I would expect the AMD processors to end up runing quite a bit slower though.