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fold and dock protocol not working

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fold and dock protocol not working

Hi, Rosetta community

I'm learning to use the "fold and dock" protocol and I tried the demo(rosetta_tests/integration/tests/fold_and_dock). My output file showed a trimer configuration but the protein was not folded(pdb file attached to this post). Could anyone tell me how to fix this?

My command script is:


setenv workdir /Users/ytao/Apps/rosetta/rosetta_tests/integration/tests/fold_and_dock

cd $workdir

mpiexec -np 2 $rosettaBin/minirosetta.mpi.macosgccrelease @flags -database $rosettaDB -run:constant_seed -nodelay > log

My flags are (same as the demo file):

-run:protocol broker
-broker:setup input/setup_init.tpb
-symmetry:symmetry_definition ./input/symm_def_trimer.dat
-fold_and_dock:rigid_body_cycles 1
-fold_and_dock:rigid_body_frequency 5
-run:test_cycles ## Remove to run a real case prediction
-score:weights score13_env_hb
-abinitio::recover_low_in_stages 0
-abinitio:rg_reweight 0.001
-abinitio:use_filters false
-packing:ex1:level 1
-packing:ex2:level 1
-packing:extrachi_cutoff 0
-in:file:fasta ./input/2akf_.fasta
-in:file:frag9 ./input/aa2akf_09_05.200_v1_3
-in:file:frag3 ./input/aa2akf_03_05.200_v1_3
-evaluation:rmsd_target input/2akf.pdb
-evaluation:rmsd_column _
-nstruct 1
-out:file:silent_struct_type binary
-out:path:pdb ./
-out:file:silent 2akf.out
-out:level 500

Never mind. I forgot to remove "-run:test_cycles ## Remove to run a real case prediction" in the flag file. Now it's running properly.

S_0001.pdb_.txt129.17 KB
Post Situation: 
Mon, 2012-11-26 15:33

I would also point out that -nstruct 1 is never a real case - generally start at 10000 for a small prediction set.

Mon, 2012-11-26 16:30