we are trying to dock two partners, and we want to rebuild a loop of one of the partners. We searched into the README.pose_docking file, and we found:
-----------extract from the README----------------------
D. To perform a small perturbation docking interating between loop
rebuiding and docking. Brief, the protocol will first remove the defined
loops from the complex, and then carry out low-resolution docking
without those loops. Afterwards, the loops will be rebuilt onto the
docked model in the low-resolution and the full-length model will
undergo fullatom docking rigid-body refinement and loop refinement.
$> rosetta.exe aa 1brs 1 -s 1brs.rlx -dock -pose -loop -fast -dock_mcm -dock_pert
8 8 8 -unboundrot -dock_rtmin -ex1 -ex2aro_only -find_disulf
-----------end of the extract---------------------------
We tried these options, but rosetta crashes with this message:
>WARNING!! .dat file not found!
>Looking for fasta file: ./mod1_.fasta
>fasta file not found!
>setup_protein_sstype: query sequence not defined !!!
>fasta file needed to read in psipred prediction !!!
>query sstype will not be defined in this run !!!
we went a bit further adding the -use_pdbseq, but now it crashes with this message:
>[T/F OPT]Default FALSE value for [-handedness_score]
> DAMN: read_fragments can't locate ./aamod1_03_05.200_v1_3
What are we doing wrong ? BTW, we were able to run loop minimization example C in the same README.pose_docking file, using:
$> rosetta.exe aa 1brs 1 -s 1brs.rlx -dock -pose -loop -minimize_loop
-dock_mcm -dock_pert 8 8 8 -unboundrot -dock_rtmin -ex1 -ex2aro_only
by appropriate definition of the [start].pose_loops file.
Any help really appreaciated, we are stacked here since a few days...