The problem hasn't been solved
Hi,
I want to use rosetta to refine my NMR structure. Could someone tell me what is the rosetta format in pdb files, and how to add missing N- and C-term residues to my generated structure? Thank you very much.
Best regards,
ddg_monomer doesn't seem to work well with mpi. I would like it to send it a job with a large amount of mutation combinations and use the mpi enabled version to finish the job quickly.
Consider the following protocol:
mpirun -np 4 /rosetta3.3/rosetta_source/bin/ddg_monomer.mpi.linuxgccrelease @ddg.flag -in:file:s min_cst_0.5.input.pdb -constraints::cst_file ca.ca.dist.cst -ddg::mut_file example.mut -ddg::iterations 50
#example.mut is a simple mutation, for instance a Leu to Ala mutation on res 1
total 1
1
L 1 A
Hi Everyone!
I'm Ben, I'm new here. I'm working on re-designing the binding pocket of an amino-acid binding protein for it to bind a new ligand. For this, I use enzdes. I want to compare the designs Rosetta makes with the wt protein in terms of binding energy (i.e. ligand-protein surface interaction energy) as a control. My question is: Is ligand docking the right application for this?
My plan in detail:
Hello all,
I am working on a script that takes a given cleaned (using the cleaning.py script) pdb file (attached as dG_calc.txt) that mutates each residue through the sequence of amino acids and calculates the dG and ddG. This is based on the ala_scan.py script except no docking or other things.
I had a couple of questions:
1) Does the mutate_residue in PyRosetta 2.0 repack the side chains automatically? If so to what distance?
2) If not, does PackRotamersMover take care of this? If I need to use this I should restrict the packer so it only uses the original amino acids?
Hi Rosetta's List,
Has anybody happen to know how the minirosetta threading protocols works?
How would I use multiple cores on a single machine in an effective way without mpi?
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?
Hello,
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
Hi
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!
Dear colleagues,
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 2.6.27.19, 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
