AbinitioRelax Disulfide Bonds are not being retained

Hi All,

I am using Rosetta AbinitioRelax, and for the most part, it seems to be going alright. However, when I introduce a disulfide bond, the application executesas normal, yet does *not* seem to retain the disulfide bond. I have seen this complication elsewhere on this forum, but there doesn't seem to be any correct advice on how to solve the problem.

My flags are:
-database $DATABASE
-in:file:fasta sequence.fasta
-in:file:frag3 fragments.3
-in:file:frag9 fragments.9
-in:fix_disulf disulfide.ss
-in:file:fullatom
-out:nstruct 10000
-out:file:silent structures_silent.out
-use_filters true
-psipred_ss2 ss2.psapred_ss2
-abinitio::increase_cycles 10
-abinitio::rg_reweight 0.5
-abinitio::rsd_wt_helix 0.5
-abinitio::rsd_wt_loop 0.5
-relax::fast
-no_prof_info_in_silentout

And my disulfide.ss file looks has the contents
1 40
(containing a new line at the end of the file as advised by one of the posts).

Note, this is the first and last residue in the sequence

Upon running AbinitioRelax, output contains the lines:
core.io.raw_data.DisulfideFile: Fixing a disulfide between 1 and 40
core.io.raw_data.DisulfideFile: Fixing a disulfide between 1 and 40

So it looks like it found the correct disulfide bonds (why there are two outputs, I have no idea).

However, all of the 10000 outputted structures are *not* restrained by disulfide bonds at the ends.

Does anyone have any idea how to get AbinitioRelax to respect the disulfide bond restraints???

Any advice would be helpful. I'm at a loss here, and the suggestions thus far don't seem to be helping.

Cheers,
Brett