The script file for execution of RNAGA includes following steps:
Put all input files in the same path (or directory) before running the job Make correct links between I/O units and the corresponding I/O files. It includes input sequence (rnaga.seq or rnaga.lib) and controling file (rnaga.in) and all files of energy table used in programs. The input files include ergparm, cf20, cf30, cf50, cf100 and cf150. The output files include fort.2 that is connected to a *scr file and fort.4 that is connected to the main output, a *cm file for predicted common structures To set unlimit for your machine because the program use huge stack size that is often greater that the normal size was set in your computer. Execute the job on /usr/tmp/~users if you have big files. Return Outputs (fort.2 and fort.4) in the correct path.