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loop modelling/Rosetta 3.4, 3.5

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loop modelling/Rosetta 3.4, 3.5
#1

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

Post Situation: 
Tue, 2013-07-02 08:38
berk

Hi berk,

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

Tue, 2013-07-02 11:32
jadolfbr

Hi Berk,

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

Thanks.

Tue, 2013-07-02 11:45
rmoretti

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 \

Tue, 2013-07-02 13:20
berk

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

try using -s instead of -loops:input_pdb

Wed, 2013-07-03 08:46
kronckbm

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

Sat, 2013-08-24 00:03
MRH