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3.8 Energy file input

Six files containing energy information are needed to run the program. The dangle energy file contains energies for single base stacking. The loop energy file contains destabilizing energies for internal, bulge, and hairpin loops. The stack energy file contains energies for base pair stacking. The tstack energy file contains energies for terminal mismatched pairs in interior and hairpin loops. In future, this file will be split into 2; one for interior loops and one for hairpin loops. The tloop energy file contains a list of distinguished ``tetraloops'' [28] that the program recognizes, and the bonus energies used to bias their occurrence. Finally, the miscloop energy file contains some miscellaneous energies related to multi-branched loops and asymmetric interior loops. The default names for these files are dangle.dat, loop.dat, stack.dat, tstack.dat, tloop.dat and miscloop.dat, respectively. These files come with the program, and simulate folding at 37° C. Folding at different temperatures is discussed in (5.6).

After these files are read, program execution continues with output file and format selection (3.9) for a regular run, and proceeds directly to the main menu (3.10) in a save run.

Michael Zuker
Thu Nov 2 14:28:14 CST 1995