The problem hasn't been solved
I am attempting to relax a glycosylated protein into a cryoEM map and get the following error:
"mpirun noticed that process rank 2 with PID 8288 on node imsb0632 exited on signal 9 (Killed)."
I get this error with both mpirun and mpiexec.
Can anyone explain more about what is causing this issue?
Hi all,
we are trying to run protien -ligand docking. We were able todo succesfully the tutorial and do for some of our drug molecules except "Diltiazem". we generated conformers using online tool [mentioned in the tutorial] and tried schrodinger conformers too. but the following error still persists. Screen shot is attached.
'Translate' mover" chain X doesnot exist.
We checked the conformers pdb file every conformer is seperated by 'TER' text and both PDB and conformers file has chain X.
Hi, I am new to PyRosetta and I have just installed it.
I want to load a pose using 'pose_from_pdb' but the following error occured:
I would like to load a residue type from a string of a params file and not a filename.
I can generate a mutable residue type, but get stuck there:
I would like to run a design protocol on a protein that has, as its asymmetric unit, 2 proteins with an ion. I have done some purely AA-based symmetric design before with 2 chains controlled by separate virtual jumps and my own python-generated symdef file but I'd rather avoid doing that again :-)
My hope was that I could put (even if suboptimal) the 2 chains and the ion in a single chain and proceed as usual in symmetric design with one chain.
Hi all,
AHo is Required for Antibody Design protocols, the antibody pdb file should be renumber in AHO using PyIgClassfiy.py
But I can't find the file “PyIgClassfiy.py”, where is it?
thanks all.
Hi all,
We downloaded Complex of a camelid single-domain vhh antibody 2P43, used Discovery Studio to change the numbering scheme of the PDB file to Chothia, then when we want to used "antibody_numbering_converter" to change the numbering scheme of the PDB file from Chothia to AHo, an error occurred, the command we used is " antibody_numbering_converter.linuxgccrelease -s 2P43_clo.pdb -camelid true -input_ab_scheme Chothia -output_ab_scheme AHo ", the error is as follow:
Hi,
I am using AlaScan.xml to do alanine scanning for my antibody antigen complex, but when I run the script, there was error said “protocols.rosetta_scripts.ParsedProtocol: Mover Docking reports failure!”
Following is my script:
<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="interface" weights="interface"/>
</SCOREFXNS>
<FILTERS>
Hello,
I ran protein-protein Rosetta docking for 50 output structures. The I_sc of the output structures (50 structures) are so close to each other in such a way that their standard deviation is so close to zero(around 0.03). I was wondering what this means. Does it make sense MC sampling of Rosetta gives me identical results?
Thank you