Member Site Forums Rosetta 3 Rosetta 3 – General homo-oligomeric proteins………….folddock+symmetry+abinito Reply To: homo-oligomeric proteins………….folddock+symmetry+abinito



    I have the same predicament. Have you found an answer you could share?


    > Hello everyone,
    > I a looking forward to generate a homodimeric protein using rosetta abinitio with the help of fold and dock and symmetry definition files.
    > (ref to:Das R, André I, Shen Y, Wu Y, Lemak A, Bansal S, Arrowsmith CH, Szyperski T,
    > Baker D. Simultaneous prediction of protein folding and docking at high resolution. Proc Natl Acad Sci U S A. 2009 Nov 10;106(45):18978-83)
    > My command line option was:
    > /home/chaos/Download/ROSETTA/v3.1/rosetta_source/bin/AbinitioRelax.linuxgccdebug
    > -run:protocol broker
    > -broker:setup setup_init.tpb
    > -out:nstruct 5
    > -out:file:scorefile score.fsc
    > -database /home/chaos/Download/ROSETTA/v3.1/rosetta_database
    > -in:file:fasta ../3vubq.fasta
    > -symmetry:symmetry_definition ../sym_def_dimer.dat1
    > -in:file:frag9 ../ff3vuba09_05.200_v1_3
    > -in:file:frag3 ../ff3vuba03_05.200_v1_3
    > -out:pdb
    > -out:file:silent OUT_3vub
    > -out:file:silent_struct_type binary
    > -relax:fast
    > -relax:jump_move
    > -symmetry:initialize_rigid_body_dofs
    > -fold_and_dock::rotate_anchor_to_x
    > -rg_reweight 0.01
    > -run:reinitialize_mover_for_each_job
    > The protein is a dimer i.e 101 reidues in each monomer. I tried using 3vub (fasta file) with one monomeric chain and fragment library for the 101 residues (monomer). Sine, the symmetry definitions are defined, I should be able to generate a dimeric structure after the run. But, the run generates a monomeric structure. When I try using a fasta file of a dimer and fragment library for a monomer, I do not get the structure of the other monomer, since, the fragment file doesn’t contain any details about it. I shall be thankful if helped with any solution towards this.
    > Thanking you,
    > Anusmita