Reply To: Is it possible to do Abinitio folding from a linear structure.?

Okie, my cmd-line is FlexPepDocking.linuxgccrelease @flags.basic > dock.log &. Anyway, I just read the manual again and I realise that the starting structure is to be an approximate of the final complex structure that I’m expecting. If that’s the case, then it defeats my purpose in docking a linear peptide to the protein and hoping to see what and where would my final conformation of my peptide be like. So is it true that way or did I misinterpret anything.? Btw, I have added the extend_peptide flag but it seems to have no changes in the results at all.

Filename: flags.basic

-s input/complex.pdb
-native input/complex.pdb
-rbMCM
-torsionsMCM
#-lowres_preoptimize
-flexpep_prepack
#-flexPepDockingMinimizeOnly
-ex1
-ex2aro
-use_input_sc
-nstruct 20
#-unboundrot input/unbound.pdb
-database /home/u1/Programs/rosetta3.2.1_bundles/rosetta_database
-rep_ramp_cycles 10
-mcm_cycles 8
-smove_angle_range 6.0
-extend_peptide true