• Extract foldtraj-current-linux-i386-icc.tar.bz2 into a directory

tar xvf foldtraj-current-linux-i386-icc.tar.bz2
cd foldtraj

• Make a folder under foldtraj directory “mkdir ubq”
• Generate trajectory file (do not append extension “.val” to output filename). After InitTraj command, ubq.trj should be created.

InitTraj -i ubq/ubq.seq -o ubq/ubq

• Generate random structures (do not append extension “.val” to input filename or “.pdb” to output filename).

foldtraj -i ubq/ubq -b 10 -f ubq/ubqunf