I have one protein that I would like to model ab initio the final 29 residues (1 - 160 is fixed/I have the x-ray crystallography model, 161 - 189 is the region to be modeled).
I am using the following parameters:
RIGID 1 160 0 0 0
- the command I ran :
/home/users/mimi/rosetta_bin_linux_2019.35.60890_bundle/main/source/bin/minirosetta.default.linuxgccrelease @/home/users/mimi/broker.args -in:file:fasta /home/users/mimi/protein.fasta -broker:setup /home/users/mimi/protein.tpb -database /home/users/mimi/rosetta_bin_linux_2019.35.60890_bundle/main/database -frag3 aat000_03_05.200_v1_3 -frag9 aat000_09_05.200_v1_3 -nstruct 200
- Everything runs fine! The problem? Even specifying -nstruct 200, I only get 100 structures... Can someone please let me know what I'm doing wrong? Because I believe this is the right protocol (as far as I know at least... and as far as I've been reading in this forum).
The -nstruct in your command line is probably being over-ridden by something in your flags file (args file).
Look in the args file you specified: /home/users/mimi/broker.args and see if there's something like "-out shuffle_nstruct 100"