Hi: I runned Rosetta for H3_modeling 10 days ago use linux computer.
now I check the folder H3_modeling. the 10 models still in progress.
anyone know when it will finish.
Thanks a lot
Since I don't know much about your simulation environment, can you share your input files? Also, are the jobs still running, and if so, can you share a log file?
The job is still running.
Thanks here is the command I used: ( I did from model 0 to model 9)
-s grafting/model-0.relaxed.pdb \
-nstruct 1000 \
-antibody:auto_generate_kink_constraint \-antibody:all_atom_mode_kink_constraint \
-out:file:scorefile H3_modeling_scores.fasc \
-out:path:pdb H3_modeling > h3_modeling-0.log 2>&1 &
Please see attached for input and log file.
Thanks so much. Now it has been 2 weeks
Can I continue to do other task on Rossetta without finshing H3 modeling task?
You can certainly do other tasks in the meantime; this job consumes a single CPU. If you have more than one core in your machine, or available to you on a cluster, you can do whatever else you like.
You unfortuanately haven't provided the flags file that you used, abH3.flags.
Here is the contain of abH3.flags, any problem with this?
Thanks so much!
$ less abH3.flags
#more standard settings, for packages used by antibody_H3
#these are standard settings for kic/ngk
-loops:allow_omega_move true ### remove 'true' and loop::?
OK, when I try to run with those flags it tells me that I don't have fragment files; by default it's looking for a file called frag9. Are there fragment files or flags that you haven't provided yet? You could try sending me your *exact* run directory as a zipped file so this doesn't happen again.
I am unable to upload zip file. here is the link for the file.