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The problem hasn't been solved
Show I put the upper/lower restraints in one file, for instance:
# Upper distance limit
29 VAL HA 29 VAL HB 5.94
29 VAL HA 29 VAL QG2 5.51
17 ILE QD1 17 ILE HB 5.61
# Lower distance limit
29 VAL HA 29 VAL HB 3.961
29 VAL HA 29 VAL QG2 3.673
17 ILE QD1 17 ILE HB 3.743
or put them separately in two files, one for upper limit and the other one for lower limit?
I'm using the standalong version of Rosetta Antibody. I can rebuild the antibodys which are already in PDB, however, for my own sequences, I can not build them for some reasons. I checked the results of the CDR Graft procedure. I found the "FR02.pdb" was distorted. Apparently, the some atoms of H-CDR3 residues were far away from the framework. Besides, I got a "VERY LOW CONFIDENCE PREDICTION" warning on the H3 loop.
I performed the flexpep docking by first prepack the interface. Then I conduct the docking with command:
flexpep -database rosetta_database/ -s prepacked.pdb -native prepacked.pdb -out:file:silent decoys.silent -out:file:silent_struct_type binary
-rbMCM -torsionsMCM -ex1 -ex2aro -use_input_sc -nstruct 100 -lowres_preoptimize
after that, I sorted the score value and select the top 5 decoys. (Is this the common way to select the decoys?)
But How can I further dock the decoys to refine the conformations? ( Do we usually refine the initial docking conformations?)
I'm currently experiencing some troubles while using the RigidBodyMovers and I hope someone could explain me this strange problem. I perform a rigid body move and calculates its energy. But the result is different if I evaluate the energy after having stored the pose in a .pdb. Here is the code.
// Creating the poses and the scoring function
core::pose::PoseOP pose = new core::pose::Pose();
core::scoring::ScoreFunctionOP score_fxn = core::scoring::ScoreFunctionFactory::create_score_function("standard");
I am running Abinitiorelax for protein structure prediction through submission script
. I find that every time I run it, the score file gets made by the name "score.fsc" in the home directory only.
How can I specify a name for this file and its output destination.
The commandline is:
$/home/xxx/Rosetta3.1/rosetta_source/bin/docking_protocol.cygwingccrelease @flags -database /home/xxx/Rosetta3.1/rosetta_database/
The content of flags is:
-s /input/1brs.pdb (I also tried various formats and locations of directories for 1brs.pdb, none of them worked)
-dock_pert 3 8
-mute core.util.prof ## dont show timing info
Before getting this error message in running rosetta, I had many troubles in the installation.
I am very new to the peptide flexible docking. When I use the locally installed rosetta 3.2.1 to perform a peptide docking. I got the error as :
ERROR: total_residue() != 0
ERROR:: Exit from: src/core/pose/Pose.cc line: 1369
The command line is :
FlexPepDocking.linuxgccrelease -database /usr/local/src/rosetta_database/ -s renum.pdb -flexpep_prepack > flex.log
I also attached the pdb file and log file.
Hope you can help me out! thank you so much!!
I got a problem when I tried extracting pdb from silent file in the tutorial in Abinitio Modeling (http://www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide/app_...). Actually I got nothing when I tried that command to exact pdb out. And there is no error message coming out, which I thought is very strange.