loop modelling/Rosetta 3.4, 3.5

[Anonymous]

Hi,

I run the loop modelling script with *Rosetta 3.4* and it works. But when I employ the same script
with *Rosetta 3.5*, I face with this error:
**exceeds the number of residues in the Pose: pose_index_ = 141 vs pose.total_residue() 0***

Cheers,
Berk

[Anonymous]

Hi berk,

Can you be more specific – which script? A RosettaScript from the demos or the loop_model application?
What are your inputs?

[Anonymous]

Hi Berk,

Could you post the commandline and input files you use which are giving you this behavior?

Thanks.

[Anonymous]

My Loop,
LOOP 141 154

mpirun.lsf /RS/progs/rosetta/3.5_gcc_openmpi/bin/loopmodel.mpi.linuxgccrelease
-database /RS/progs/rosetta/3.5_database
-loops:input_pdb inputs/Drd2.B99991000.pdb
-loops:loop_file inputs/Loop.file
-loops:frag_sizes 9 3 1
-loops:frag_files inputs/aat000_09_05.200_v1_3.gz inputs/aat000_09_05.200_v1_3.gz none
-loops:remodel quick_ccd
-loops:remodel perturb_kic
-loops:refine refine_kic
-loops:fix_natsc true
-loops:neighbor_dist 0.0
-loops.max_kic_build_attempts 100
-loops:extended
-ex1
-ex2
-out:pdb
-out:prefix TEST
-out:file:fullatom
-nstruct 1000
-out:overwrite

[Anonymous]

I’m relatively new to rosetta, but I think this might help:

try using -s instead of -loops:input_pdb

[Anonymous]

Thats great , worked fine in my case. Thank you.

[Author]

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