modifying the source to mfold or other rna folding program is
your main option. The reason large molecules like 2.5kb are not
normally supported is that it takes a huge chunk of memory
for a program to deal with rna folding that size, and a lot
of cpu time. Be prepared for a good long wait, depending
on how fast your computer is, for the results. I think analysis time
is proportional to the cube of the size of the molecule.
Your GCG version of mfold source is likely on your computer
in the gcg/source location. But if you can't find it, you can
dig up Michael Zuker's original mfold source at this ftp location:
-Michael Zukers software for folding with multiple suboptimal
scores, viewing of structures and more.
-- d.gilbert--biocomputing--indiana u--bloomington--gilbertd at bio.indiana.edu