The problem hasn't been solved
Hi, All:
We just compiled opencl version of rosetta. But when I run rosetta_scripts.opencl.linuxgccrelease, there is no running processes found in GPU. I am just wondering if GPU is supported after opencl version is successfully compiled. Thanks.
Best,
dear rosetta users.
Dear Rosetta Community,
I am trying to generate conformations for a 29 residue cyclic peptide with N-C terminal cyclisation. I've written a Rosetta Script that declares a bond between the N and C terminals and then performs a loop closure based on GeneralizedKIC.
However I am facing the following error:
I have a question regarding Pyrosetta. Currently, I want to use pyrosetta to score some protein structures but with missing atoms in sidechain. So my protein structures contrain full-atoms for backbone but missing one or two atoms per residue on sidechain. I used pose_from_pdb to read my protein structure (pdb). But it seems pysoretta will fill in the missing atoms according to rotamer library. Is there a way to prevent it so I can just score my structures with missing atoms on sidechains?
Thanks a lot for the help,
Hello,
I want to model the tetrahedral transition state of an enzyme where serine OG attacks the peptide backbone C atom. In this case the bond order of the backbone C=O bond changes to C-O(H) and the C-O(H) is not in plane anymore.
So far I wrote this patch file and added a hydrogen to the O atom in the input model which is named H01. The patch file is used since I get an error when I don't include it.
BEGIN_CASE
BEGIN_SELECTOR
NAME3 LEU
END_SELECTOR
A pose can have a constraint set, a modifiable residue set, an unnoticed `pose.pdb_info().obsolete() == True` case, virtual residues, energies and a few more. Therefore when saving to disk none of the following truly work as they save coordinates:
pose.dump_pdb('foo.pdb')
pose.dump_scored_pdb('foo.pdb', pyrosetta.get_fa_scorefxn())
pose.dump_cif('foo.cif')
pose.dump_mmtf('foo.mmtf')
pyrosetta.io.poses_to_silent([pose], 'foo.silent')
So I was hoping for an all-in-one
Hello,
I was working on homology modeling and built 1000 models with ligands. I'm planning to select 100 top scored models and do clustering on them.
I tried cluster.linuxgccrelease, but the program didn't recognize the ligand. I specified the option -exclude_res, but it didn't work.
I also tried calibur.linuxgccrelease, but there are a lot of warnings instead of the output.
I'm attaching the log files. Can you help me with these issues? Thank you in advance!
The above tells me that an RNA low-resolution potential
(rna_lowres_sf = core.scoring.ScoreFunctionFactory.create_score_function("rna/denovo/rna_lores_with_rnp_aug.wts"))
Where is the best place to create a sequence profile for rosetta fragment picker?
I am trying to use the makefragments.pl to get a sequence profile for 1203 residue monomer of the sars-cov-2 spike protein and Ive run into a error about SS0 predictor. Im using this command line
make_fragments.pl -verbose -psipredfile ab42c8a0-7d52-11eb-a871-00163e100d53.ss2 -n_frags 200 -n_candidates 200 -frag_sizes 3,9 sequence.fasta
I was wondering what things would make the predictor nonfunctional and if there is a physical file that I could interact with. Or if the predictor relies on files from the nr database.