The problem hasn't been solved
Dear friends,
I am using "minirosetta.linuxgccrelease" for homology modelling. It is recommended at least 1000 outputs are needed. However, after running 3 days, my PC got a problem and only ~500 outputs have been generated. If I run a second run, can I just run another 500 outputs and combine them together with the first batch outputs, and assume those 1000 outputs are generated from same batch?
In the tutorial on the loop modeling, loop is defined by the fold tree in the loaded from pdb-file pose that already have residues that are "loop" and are normally missing. If I have a structure, where the loop is missing, how do I define it? As far as I understand, there's no way to do this from sequence, Do I have to make a "fake" loop structure before obtaining a possibility to really model it?
I am using Rosetta 3.5 to predict protein structures using AbinitioRelax protocol.
When I specify -kill_hairpins I always got the following errors:
ERROR: [ERROR] invalid header input for kill_hairpins file.
ERROR:: Exit from: src/core/scoring/SS_Killhairpins_Info.cc line: 375
Exception :
[ERROR] EXCN_utility_exit has been thrown from: src/core/scoring/SS_Killhairpins_Info.cc line: 375
ERROR: [ERROR] invalid header input for kill_hairpins file.
Is it possible to suppress PDB output, but use silent output instead for the Backrub program? Rosetta <strikethrough>3.4</strikethrough> is used.
update: I am running 3.5, not 3.4.
Hi, Im new to Rosetta and these forums, but I have a problem running Rosetta. I’ve compiled on a CentOS machine, but I keep getting segmentation faults and crashes,
e.g. I try to run AbinitioRelax.default.linuxgccrelease --help
But it crashes in the midst of output with
rmsd_dump | 2 | R| dump all pdbs for loops that
| | | are below in rmsd
terminate called after throwing an instance of 'std::string'
Abort (core dumped)
Dear developers,
I'd tried to complile and install Roseta3.5 in my Ubuntu Ubuntu 12.04.3 LTS x86_64. My MPI version is MPICH2 Version: 1.4.1p1 and is installed at:
/usr/lib/mpich2/lib/libfmpich.so
/usr/lib/mpich2/lib/libmpichf90.so
/usr/lib/mpich2/lib/libmpl.so
/usr/lib/mpich2/lib/libmpichcxx.so
/usr/lib/mpich2/lib/libmpich.so
/usr/lib/mpich2/lib/libopa.so
At first I tried to compile using this options:
sudo scons bin mode=release cxx=gcc cxx_version=4.6 extras=mpi,static -j4
Hi,
I'd like to rescore protein docking decoys to calculate the Irms (interface rms) against the lowest energy decoy. If I rescore using the scoring application, I can get the overall rms but not the Irms. I've tried including flags like -evaluation:Irms but can't seem to get it to work. Also, although less important, is there away to apply the same scoring as the docking application does - without specifying any scoring patches or weights or anything the overall score is completely different to the docking output score.
Cheers.
Folks,
In September 2014 (before shellshock patch) a user ran a Loop modeling job on our system (rhel 6.3 IBM Platform HPC 4.1.1.1)
The Rosetta version is rosetta_2014.30.57114_bundle
The user is running minirosetta.mpi.
the command is:
mpiexec -launcher ssh -f /PATH/machines -n 50 -ppn 8 /PATH/rosetta_2014.30.57114_bundle/main/source/bin/minirosetta.mpi.linuxgccrelease @/PATH/DGCR8_NOE_10172014/2LZM_broker_cst.options -database /PATH/rosetta_2014.30.57114_bundle/main/database
the options file looks like this
