Thanks alot smlewis and smg3d 
I ran abinitio on 2 proteins with no errors however on 1rop protein I have the following error
protocols.jumping: compute strand/loop fractions for 63 residues…
protocols.abinitio.AbrelaxApplication: run ClassicAbinitio…..
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: standard
core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12
protocols.jobdist.JobDistributors: Looking for an available job: 1 1 1
protocols.abinitio:
===================================================================
Stage 1
Folding with score0 for max of 2000
protocols.abinitio.FragmentMover: BEGIN: 55 SIZE: 9 TOTAL_RES: 56
protocols.abinitio.FragmentMover: Are the fragments compatible with the fasta or the input PDB used to extract the folding sequence ?
protocols.abinitio.FragmentMover: It appears that the fragments go up to residue 63 while the pose only has 56 residues!
ERROR: Assertion failure: runtime_assert( ( begin + size – 1 ) <= pose.total_residue() );
ERROR:: Exit from: src/protocols/abinitio/FragmentMover.cc line: 122
I checked teh fragmentMover It says that I should switch off non continuous fragment insertions… I tried some of the options stated in -help didn’t work!
Do you have any idea how can I turn that off?
Thanks again,
Meghrig