The problem hasn't been solved
First I want to make sure that I understand this correctly. Fragmentation creates L-K+1 fragments, blasts them against some database and finds the homologous secondary structures that are shown below (small portion as an example). Correct?
I'm running Rosetta single state design (though I imagine my question applies to MSD as well), which works great on a single core or my local machine. I'm using rosetta_scripts.mpi.linuxgccrelease as my package. It is compiled by my HPC administrator to function with the cluster.
Hi eveyone,
I built Rosetta on a linux machine and it takes up 24G of space. However, I'd like to remove extra parts (like demos or pilot apps) or in any other way, reduce this space.
Is there any solution for this? Is it possible to keep the shared libraries and .so files and remove all the codes?
Thanks a lot in advance,
Hamed
Hi all,
Sorry to trouble again.
I understand that the multistate design protocol outputs structures where the chains A and B will become AA, AB and BB.
However, I get the output of chains A and B even in the output files AA and BB.
May I find out how I could produce the output files AA and BB homodimers?
Is this something to do with my corr file?
Hey all :)
Does the Rosetta force field incorporate parameters for PTMs such as hydroxyproline and C-terminal amidation? If so, where can I see this in the database? If not, how can I parameterize this?
Thanks!
Hello！
These are many .wts file in database\scoring\weights.
I don't clearly know which weight is used in which occasions,
and just use score function according to papers.
I read the webpage(https://www.rosettacommons.org/demos/latest/tutorials/scoring/scoring)
and its recommend references.
I have the following flags in my refinement flag file, I'm getting the error ERROR: Unused "free" argument specified: GDP.fa.tors, I'm not sure why!
-extra_res_cen GTP.cen.params GDP.cen.params -extra_res_fa GTP.fa.params GDP.fa.params-extra_improper_file GTP.fa.tors GDP.fa.tors
I'm trying to run python /home/labusr/rosetta/main/source/scripts/python/public/molfile_to_params.py --keep-names --clobber --extra_torsion_output --centroid gtp.mol2 -p GTP -n GTP, on a gtp.pdb that has been reduced using phenix.reduce and converted to mol2 using openbabel. Below is the error I get.
Hi,
I am currently running a multistate design protocol (mpi_msd.linuxgccrelease) for bispecific antibody design. After I have run the protocol with my options, the program runs and is "stuck" at this point for a long time:
core.pack.pack_rotamers: built 39485 rotamers at 58 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DoubleLazyInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 22325380 bytes
Hello,
I read the paper Rosetta and the Design of Ligand Binding Sites
and it enlightens me.
According to the method of this paper, I design my enzyme.
However, I find these are a few unreasonable results which show reaction atom of ligand do not close to catalytic triad,
but the opposite side of ligand close to catalytic triad.
So I want to make docking with constraints.