Member Site › Forums › Rosetta 3 › Rosetta 3 – General › the problem in making fragments
Hi I’m new user in this wiki page
I have problem in making fragament step using rosetta3.0 in CS-rosetta
which is developed in bax group for nmr structure determination
when I invoked the command make_fragment_2000.pl ( nearly same as
make fragment.pl excep the vall database and compiled pNNMAKE.gnu)
I got the following error message at the final step of fragment file making
read_vall (unit= 20): /usr/local/csrosetta/vall.dat.apr24
read homolog 18 ./t000_.homolog_vall
WARNING:: unable to find/open homolog file
read homolog 18 ./t000_.homolog_nr
WARNING:: unable to open/find homolog-nr file
not reading pdb file for t000
size 3inserts 115
size 9inserts 109
inserts stuck at 3mer pos: 8 inserts: 23
shockingly low fragment diversity for 3mers at pos: 8 inserts: 23
I treid with several other fasta file also..
but the result was same.
what could be the problem?
I don’t have a clue how to fix this fragments issue, but the Robetta fragment server might work better for you: