Reply To: homo-oligomeric proteins………….folddock+symmetry+abinito

[Anonymous]

Hi,

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

thanks.

> 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