I am trying to make fragment files for membrane_abinitio application. I have secondary structure prediction results (*.rdb files) from SAM secondary structure server. I am trying to run the command:
make_fragments.pl -nojufo -nopsipred -noprof -samfile HRG3_all_X.t2k.str2.rdb HRG3.fasta
The program is generating all the files (.cst, .a2m) but somehow its not generating fragment (frag3, frag9) files at all.
Could anyone please help in this matter ?