Hello,
I want to do a simple scoring of some docking solutions. My flags are:
-in:file:l list.txt
-score:weights docking
-out:file:scorefile scoring/score_docking.sc
... but I get this error:
[ ERROR ]: Caught exception:
Hi,
I have some questions about setting for scoring and weights. That would be really helpful if someone could answer the questions.
1.
I looked into the folder> Rosetta/main/database/scoring, there are loads of score files.I'm wondering How to choose the right one.
Should I just use one for all applications? For example, If I use Rosetta3.12, should I use ref2015.wts for relax, loopmodel,etc?
Could someone please kindly explain to me what's the difference between these score files?
Hi everyone.
We are docking small molecule ligands into non-enzyme proteins to get an idea of ligand distribution/convergence within the binding pocket, using the LigInterfaceEnergy mover. While the results are promising, ligands with the lowest LigInterface energy are sometimes outliers within the ligand distribution. There is no native structure to compare to other than the input pose.
Hi,
I'm trying to mutate and minimize a complex with atom pair constraints applied to the residues around the mutated position, but the constraints do not seem to be getting applied to my pose. This is what I have:
Hi All,
I am trying tor learn Rosetta basics using the tutorial https://www.rosettacommons.org/demos/latest/tutorials/input_and_output/input_and_output
However, when I try like it is instructed in the tutorial following error happens:
Infinity4s-iMac-2:main smbatgevorgyan$ cd demos/tutorials/input_and_output/
Hello everyone,
I have compiled rosetta with OpenMPI and MySQL. It works.
I'm using relax to pack+score a few thousand poses but the output will create lots of tables with A LOT of info. I just need to output the pose name and the total score of the pose.
I was wondering which flags should I use (@relax.flags) to output only the SCORE table to MySQL, not the atom coordinates and the rest of the info.
By this I mean the same info as the default.sc file, but sent to a single table in mysql.
Thanks in advance.
Hi,
I am trying to load a structure from PDB and then calculate pairwise residue energies between residues in the structure. For this, I want to first load the scorefxn and then the structure (or viceversa), but whenever I try, either of them gives me a segfault, i.e. if I do scorefxn = get_fa_scorefxn(); pose_from_pdb() the latter crashes and if I do the opposite, get_fa_scorefxn() crashes.
In the supplementary material of the all-informative 2015 JChem paper The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design there is one detail that I do not understand and was curious about. Namely, "Rosetta predictions of density, heat of vaporization (∆Hvap) and heat capacity (Cp(l))".
I am trying to build glycans into a cryoEM density following the Meiler Lab tutorial here: http://www.meilerlab.org/jobs/downloadfile/name/Apr2019_glycan_modeling_talk.pdf
Using the provided XML file, I am able to run the job, but I see the following warning throughout the output file:
0mcore.scoring.electron_density.FastDensEnergy: ^[[0m^[[1m[ WARNING ]^[[0m Fold tree is not set properly for density scoring!
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?
