I do fragment-based loopmodeling which is performing well. Now I want to add a distance constraint to have a disulfide bond between two cysteines but something is going wrong and I get no output. What am i doing wrong?
My input file is:
mpirun -np 10 /opt/soft/rosetta3.4/rosetta_source/bin/loopmodel.mpi.linuxgccrelease -in:file:fullatom -loops:input_pdb mc4.pdb -loops:loop_file mc4.loop_file -loops:frag_sizes 9 3 1 -loops:frag_files mc4_09 mc4_03 none -loops:remodel quick_ccd -loops:refine refine_kic -loops:relax fastrelax -loops:extended -loops:ccd_closure -loops:random_loop -in::file::psipred_ss2 mc4.psipred_ss2 -nstruct 10000 -constraints:cst_file mc4.cst -constraints:cst_weight 10.0 -out:file:silent mc4_silent.out -database /opt/soft/rosetta3.4/rosetta_database
and the constraint file is:
AtomPair SG 257 SG 263 HARMONIC 2.0 0.1
What should I change?
Thank you very much in advance!