mkdir fragments
mkdir: cannot create fragments.
fragments: File exists
make: [fragfinder] Error 2 (ignored)
cd fragments ; \
	/cse/grads/rachelk/sum00/fragfinder/src/fragfinder t124 -i ../T0124.t2k-w0.5.mod -db /projects/compbio/experiments/models.97/select-sets/dunbrack.seqs -fraglen 10 -numpermatch 6 -alignfile ../T0124.seq 
Reading parameter file ../T0124.t2k-w0.5.mod
../T0124.t2k-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17304/tmp.a2m
SAM: /cse/grads/rachelk/sum00/fragfinder/src/fragfinder v3.2 (June, 2000) compiled 08/28/00_17:51:26
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  ../T0124.t2k-w0.5.mod
make: *** [fragfinder] Error 1