The problem hasn't been solved
Im modelling a camelid antibody (vhh) amino acid sequence using Rosetta (rosetta_src_2016.32.58837_bundle). I cannot generate these input files : "FR02_H.pdb", "FR02.cst", "FR02.cst_fa". Please tell me which 'bin' sould I use to get this inputs for "camelid antibody graffeting". Thanks.
I am running the example protocol (RosettaCM multi-template comparative modeling) supplied by the Meiler lab (I think?). Only I am using a different starting protein that the one provided. I have successfull made it to the hybridize step:
Hi,
I am using Rosetta local refinement to calculate the interface scores of known protein complexes (in a bound form).
In the docking protocol, it says "Typical values for I_sc of godd decoys are in the range of -5 to -10.". However, for some complexes, rosetta local refinement gives me I_sc as low as -5988.1. This number doesn't seem realistic to me. Could you please explain why we see such small numbers? How can we interpret this result, if the good binding score is in the range of -5 and -10?
I am trying to calculate rmsd using a template pdb structure using score_jd2. When I try to run the following command,
$ROSETTA3/bin/score_jd2.macosclangrelease -in:file:silent decoys_alp_tcn.out -evaluation:rmsd 2alp.pdb `cat pdb_list` FULL -out:file:silent rescored_decoys.out
it errors out saying ERROR: Unrecognized residue: SO4. Then I rerun the same with -ignore_unrecognized_res
Then I get the following error:
ERROR: [ERROR] Error opening RBSeg file 'batch_000065_000059'
I am trying to run a very simple threading scenario (comparative modeling - but as basic as it gets).
I am executing the command:
partial_thread.static.linuxgccrelease -database $ROSETTA_DATABASE -in:file:fasta /inputs/2yhd_model.fasta -in:file:alignment /inputs/2yhd_model.grishin.txt -in:file:template_pdb /inputs/2yhd.pdb
But an getting the error:
Hi,
I am designing a protein-protien interface using Rosetta Scripts, and would like to use logic in the resfile.
For example, if one amino acid at a given position is re-designed to be [list of aa], then the redesign at this other defined position should be limited to [list of aa]
Is this possible?
conway2016 correction was shown to be a useful improvement when applied to talaris2014. I just wonder if it makes sense to apply it to the new generation of scoring functions, say, beta-nov15 in Rosetta3.8 ?
Hi,
I'm following the antibody modeling protocol recently published in Nature Protocols "Modeling and docking of antibody structures
with Rosetta". I run into an error when running snugdock with ensembles. I get a segfault (last couple lines posted) with no additional info. However, if I don't specify to run with ensembles, the snugdock run proceeds to completion. I'm using rosetta3.8.
~/rosetta/bin/snugdock.linuxgccrelease @snugdock.flags
tail of output: