Memory Leak: Relax Density MPI RAM overusage kills process
Submitted by mmfarrugia on Sun, 2023-12-31 12:02
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Broken structure of local docking of replicadock2
Submitted by Jun on Thu, 2023-12-28 00:26
Category:
Docking
Hello, I tested local docking of AlphaRED (ReplicaDock2) protocol. As the mc steps, the fa_rep score increases rapidly.
Checking a trajectory with high fa_rep score, there are clashes between some residues. (e.g. 1st score and 2000th score)
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Error when running the CstfileToTheozymePDB Application
Submitted by jkoch19 on Mon, 2023-12-18 08:34
Category:
Enzyme Design
Hello,
I am relatively new to Rosetta, and i am trying to generate a constraint file (.cst) with my catalytic amino acid and ligand defined, that i am going to use to search against a PDB database. However, no matter how hard i try i keep obtaining this error:
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rosetta install failure
Submitted by paulbo on Wed, 2023-12-13 05:20
Category:
Compilation
hello, I seem to meet the same problem on ubuntu22.04 install rosetta_new_daily_release https://www.rosettacommons.org/node/10991. I used the command sudo apt install python-is-python2,but wrong in connect python2 candidate. So i used sudo apt install python-is-python3. And type the comand "./scons.py -j 12 mode=release bin extras=mpi" ,but wrong :
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Academic email verification
Submitted by ssrn on Tue, 2023-12-12 05:14
Category:
ROSIE
Hi,
Could you please verify my academic email address so that I can access ROSIE via Github?
My institution name : Université de Rennes
My institution domain is : @univ-rennes.fr
Best
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Error when running AqueousPoreFinder protocol
Submitted by mluengo on Mon, 2023-12-11 02:55
Category:
Membrane
Hi,
I am currently trying to run a FastRelax protocol for a pore protein (4tsy) with an implicit membrane. To define the membrane I have been using the RosettaMP implementation. However, when running the AddMembraneMover I get the following segmentation fault during the AqueousPoreFinder protocol:
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Installing rosetta.source.release-362 with MPI
Submitted by mb0261 on Fri, 2023-12-08 05:56
Category:
Compilation
Greetings,
I'm trying to compile rosetta on my $SCRTACH directory in a HPC using a conda environment (Python 3.7) to use Scons. But all I get is the following error message:
scons: *** [build/src/release/linux/3.10/64/x86/gcc/12.2/mpi/AbinitioRelax.mpi.linuxgccrelease] TypeError `File /shared/software/cuda/11.7/lib64/libcufft.so.10 found where directory expected.' trying to evaluate `${_concat(LIBDIRPREFIX, LIBPATH, LIBDIRSUFFIX, __env__, RDirs, TARGET, SOURCE)}'
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analyze_flex_ddG.py
Submitted by valebut on Tue, 2023-11-28 04:30
Category:
Chemically Modified Residues
Hello,
I am new to Rosetta. I am trying to perform the Flex ddG tutorial in order to predict changes in binding free energies upon mutation (interface ΔΔG).
I downloaded the folder from the GitHub webpage, and I succeesfully ran the run_example_1.py script which has generated three folders with one rosetta.out files (along with other files).
Then, I ran the python3 analyze_flex_ddG.py output/ command, and I get this error:
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I want to refine my pdb file,but it has multiple breaks or has multiple loops missing resi
Submitted by Edward on Sat, 2023-11-25 04:58
Category:
Loop Modeling
Take 6A5E for example,it has multiple breaks. i try to feed a blueprint file with all loops,however it turn out only the first loop was remodel .guess what when i view it in pymol i still got the same number of break .
here is my command$> mpiexec -np 18 remodel.cxx11threadmpiserialization.linuxgccrelease @missing_resi_loop
and my flag file
-loops
-in:file:s FER-LLG2.pdb
-remodel:blueprint ferllgb.remodel
-run:chain B
-remodel:num_trajectory 1
-remodel:quick_and_dirty
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Error with SapScoreMetric (SimpleMetric sap_score not found in basic::datacache::DataMap)
Submitted by Seongsung on Fri, 2023-11-24 05:09
Category:
Scoring
Hello, I encountered an error while attempting to use the 'SapScoreMetric' in RosettaScript.
I encountered the following error, but when I exclude the 'SapScoreMetric' parts, it works well.
---------------------------------------------------------------
[ ERROR ]: An issue with your Rosetta run was detected
Please correct the following issue and retry:
SimpleMetric sap_score not found in basic::datacache::DataMap.
---------------------------------------------------------------
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