I read more about rosetta and came up with this command line for denovo structure prediction of 382 residue long protein:
I ran it in silent mode.
mpiexec -np 16 ../../main/source/bin/AbinitioRelax.mpi.linuxgccrelease -database ../../rosetta/rosetta_src_2019.31.60840_bundle/main/database/ @options -mpi_tracer_to_file log1 & options: -in -file -fasta sequence.fasta # protein sequence in fasta format -frag3 t001_.200.3mers # protein 3-residue fragments file -frag9 t001_.200.9mers # protein 9-residue fragments file -abinitio -relax -increase_cycles 10 # Increase the number of cycles at each stage in AbinitioRelax by this factor -rg_reweight 0.5 # Reweight contribution of radius of gyration to total score by this scale factor -rsd_wt_helix 0.5 # Reweight env, pair, and cb scores for helix residues by this factor -rsd_wt_loop 0.5 # Reweight env, pair, and cb scores for loop residues by this factor -relax -fast # At the end of the de novo protein_folding, do a relax step of type "FastRelax". This has been shown to be the best deal for speed and robustness. -out -nstruct 50000 # how many structures do you want to generate? Usually want to fold at least 1,000. -file -silent abrelax.out # full path to silent file output -silent_struct_type binary # we want binary silent files -scorefile score.sc -overwrite # overwrite any existing output with the same name you may have generated -nstruct 50000
the program is running on 16 cores and has generated log files like this:
log1_0, log1_1, ......log1_15
. Can you please let me know if this is correct? And, once the program finishes then how to analyse the silent files since there are multiple files like this, abrelax_1, abrelax_15 etc to find best 3D structure? I am following this tutorial for abinitio structure prediction: