The problem hasn't been solved
Hi,
I would like to apply BackrubMover not to the whole protein as it is by default but the fragment of the protein (not contiguous in sequence). How can I specify this in PyRosetta?
Could you please write me the example command.
Thanks!!!
AOK
Deal ALL,
What's the difference between between score and bk_tot? The website says that "
score: the total score using the all-atom (high-resolution) energy function (lower is better)
bk_tot: total score used in the side-chain packing algorithm".
But I still confused. Which one the real energy of the protein structure? Is that lower bk_tot always has lower "score"? Thank you!
Hi all,
A short question..... Can I use ATOM as ligand instead of HETATM for the ligands in the ligand_dock application? How can I do that if it is possible?
Thanks~
In Rosetta 3.4, the fragment picker puts out a new format. AbinitioRelax does not recognize it. I get this error:
ERROR: no fragment to compute secondary structure
ERROR:: Exit from: src/core/fragment/SecondaryStructure.cc line: 68
If I run exactly the same command but with the old style fragment files, it works fine. Is there something I'm missing?
Hello!
Im trying to write a de novo folding script with pyrosetta (PyRosetta
v2.011 for windows).
I'm trying to follow the approach described in this paper:
Alena Shmygelska and Michael Levitt; Generalized ensemble methods for
de novo structure prediction, PNAS February 3, 2009 vol. 106 no. 5
1415-1420
that in turn refers to
Rohl, et all; Protein Structure Prediction using Rosetta, methods in
enzymology vol 383, 2004.
Right now I'm using only low resolution centroid score functions
because I'm not interested in the all-atom refinement stage in my project
Hi,
What would be the most suitable procedure to model ab initio a long linker (~60 aas) between two protein domains, which structures and relative positions are knowns? This linker is missing in an X-ray structure of the protein, and has no homology in the pdb.
Is it possible to model the whole protein by homology on the X-ray template, build the linker, and then optimize only the linker while "freezing" the rest of the protein?
Thanks in advance,
Isaure
Hi Rosetta users,
Has anybody happen to know if Rosetta's ddg_monomer can deal with a null mutation (deletion)?
I've read that ddg_monomer cannot handle mutations to cysteine. Please, could someone tell me why? Also, is there a overcome to analyse mutations to cysteine?
All the Best,
Fred
Greetings,
I would like to dock a small protein (59 amino acids plus one 140 atom ligand) to a large trimeric complex (358 amino acids *per monomer*, plus eight 140-atom ligands). The total number of atoms in the system is nearly 21,000.
When I run a small test of the system using the following flags (we use Torque for queuing jobs) and generate 10 decoys per instantiation, each decoy takes between 1800 and 2400 seconds to complete (30-40 minutes).
command:
/pathto/bin/docking_protocol.linuxgccrelease
flags:
-in:path /pathto/rosetta_database/
Greetings,
When trying to dock two proteins (with ligands), I obtained the following error:
can not find a residue type that matches the residue PRO_p:pro_hydroxylated_case1at position 31
ERROR: core::util::switch_to_residue_type_set fails
ERROR:: Exit from: src/core/util/SwitchResidueTypeSet.cc line: 135
When I review the log file, I see the following:
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 4219 residue types
Hi,
I'm fairly new to using Rosetta suite, so sorry if silly questions. I'm running ddg_monomer app for a protein of about 150 aa.
A) the pdb outputs I get are all the same, there is no backbone or sidechain movement neither for wt nor for mut structures (50 for each as recommended). I intended to carry out the protocol of row 16 in Kellogg, 2011. I attached the options file, if you'd be so kind to take a look at it. What am I missing here?
