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the problem in making fragments

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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 ( nearly same as

make 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
vall_size 2330105
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
make_dat 16./t000.dat
not reading pdb file for t000
size 3inserts 115
size 9inserts 109
merging fragments
inserts stuck at 3mer pos: 8 inserts: 23
shockingly low fragment diversity for 3mers at pos: 8 inserts: 23
nnmake failed!

I treid with several other fasta file also..

but the result was same.

what could be the problem?

Thu, 2009-12-03 17:15

I don't have a clue how to fix this fragments issue, but the Robetta fragment server might work better for you:

Fri, 2009-12-04 06:59