homology membrane modeling demo in rosetta 3.5

Hi everyone,

I know this is a simple question but I’m having a lot of trouble and I haven’t found the answer. I’m using rosetta 3.5 and I’m attempting to model a ion channel that has homology with a crystal structure found on pdb. My goal is to do homology modeling of several membrane passes then loop/abinitio modeling on about 100 amino acids in the c-terminus. I’m attempting to follow the instructions given in the rosetta_demos/membrane_homology_readme, however, that file does not specify what rosetta executable in the rosetta_source/bin file to use. I attempted to make all the input files and used all the flags recommended. I have tried minirosetta and loop modeling with no success, my model always comes out as a straight alpha-helix with coil-coil at the ends. My protein of interest is supposed to have two membrane passes with a membrane dip in-between the two, and an unknown modeling of the c-terminus of 100 amino acids.

files:
I am using pdb 2r9r as a template
./../rosetta_source/bin/loopmodel.default.linuxgccrelease
-database ../../rosetta_database
-in:file:fasta kv74225.fasta
-run:protocol looprelax
-loops:frag_sizes 9 3 1
-loops:frag_files kv74225_09_05.200_v1_3 kv74225_03_05.200_v1_3 none
-loops:input_pdb out.pdb
-loops:loop_file kv74225.loopfile
-in:file:spanfile kv7-4.span
-out:file:fullatom
-out:file:silent_struct_type binary
-out:file:silent kv7-4-homology_${1}.out
-nstruct 10
-loops:remodel quick_ccd
-loops:random_loop
-loops:idealize_before_loop_close
-loops::relax fastrelax
-fail_on_bad_hbond false

I’ve also run this using the loop_modeling executable.

Please let me know if you need any more information

Thanks again,

Ryan