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The problem hasn't been solved
My code creates protein models that need to be relaxed in order to lower their energy as these models may have some close contacts and other non-protein like features. According to the online documentation, the Rosetta command for relaxing non-idealized structures is
rosetta.exe aa xxx_ -relax -farlx -minimize -s xxx.start -fa_input -fa_output -use_input_bond
My questions are: 1) Is this the correct command for relaxing my models and make them "fall" in the nearest local minimum? 2) If so, how can I call these functions from inside my C++ code?
I am attempting to use the Enzyme Design application to redesign a ligand binding site to accept a different ligand. I am running the following command:
$ROSETTA33/bin/enzyme_design.linuxgccrelease -database $ROSETTA33/rosetta_database -in:file:s input.pdb -in:file:extra_res_fa LG2.cen.params LG2.fa.params LG1.cen.params LG1.fa.params -enzdes:cstfile constraints.cst -enzdes:detect_design_interface -enzdes:cst_design
I have a silent file of 20,000 decoys and I want to extract/separate low energy decoys out to a separate silent file for all atom relax. Is there any possibility of doing it. I tried cluster.linuxgccrelease with -cluster:output_score_filter and it doesn't seem to work! Is there any workaround or possibilities of any script!
I am trying to install Rosetta 3.3 on:
- HP ProLiant DL380 G6
- CPU: 2 x Intel Xeon Quad Core
- OS = SUSE SLES 11, kernel 188.8.131.52, x86_64
- compiler: gcc 4.3-62.198-x86_64
- python: 2.6.5
- scons: 2.1.0
command: scons bin mode=release
crash + error message:
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld: skipping incompatible /usr/lib/libm.a when searching for -lm
Mac OSX 10.7 - Lion 64bit
I downloaded and extracted the files for PyRosetta. I moved them to my documents. When I open terminal and go the directory where PyRosetta is located I cannot step 4 to work from the instructions online.
4. From within the PyRosetta directory, type 'source
SetPyRosettaEnvironment.sh' into the command line to set up the PyRosetta
I type "bash-3.2$ source SetPyRosettaEnvironment.sh"
I receive an error that says "bash: cd: SetPyRosettaEnvironment.sh: not a directory