The problem hasn't been solved
Hello:
I am trying to run the loop protocol by command:
mpirun -np 4 /soft/rosetta3.3/rosetta_source/bin/loopmodel.default.linuxgccrelease -db /soft/rosetta3.3/rosetta_database @flags >log &
but it said:
/usr/bin/env: python2.6: No such file or directory
anybody have any idea?
THX
Hello:
I've got a crystal structure and there is a loop region which contains 20 aa was missed. I am planning to fill in such loop by Rosetta. However, I found that there are three different methods for loop refinement in Roseeta:
Loop Modeling
Fragments Based Loop Modeling
Kinematic Loop Modeling
Do you have any idea which one is better for my case?I've complied Rosetta by command:
scons bin mode=release extra=mpi
I don't whether those refinement can be supported by mpi multiple thread.
Thank you very much
best
Hi all. Recently I've been using the FloppyTail application to try and model the N-terminal floppy region of my protein. I ran into (and solved) two issues, one that I'm sure is a genuine bug, and another that may be known but is nonetheless very serious. I am running rosetta 3.3 on a machine running MacOS server 10.5. All tests used the '-C_root' option, and had my protein listed first in the pdb.
Dear Developers,
First question!! :-
I am using DDG Monomer to calculate ddgs for some mutants. Following the paper Kellogg-2011 I use both the Row3 (Low Resolution) and Row16 (High Resolution) protocols.
Also as is recommended in the manual page for ddg monomer (http://www.rosettacommons.org/manuals/archive/rosetta3.3_user_guide/d3/d...) I iterate 50 times for both protocols.
I have two computers； the old one compiled well and the program ran well.but the new one I tried everything
and could not compile correctly.
the error line mostly like this:
/tmp/cc9VrS4H.s: Assembler messages:
/tmp/cc9VrS4H.s:31770: Error: unknown pseudo-op: `.uleb128'
scons: *** [build/src/release/linux/2.6/64/x86/gcc/protocols/toolbox/pose_metric_calculators/DecomposeAndReweightEnergiesCalculator.os] Error 1
scons: building terminated because of errors.
I have tried Ubuntu 10.10, 11.10; fedora 14, 15
gcc 4.4 4.5 4.6
change the finline-limit to 200
The fragment_picker executable barfs on carriage returns. Can something be done about this? I've added the following line to the make_fragments.pl script:
die "$file is a dos file, yuck! Get rid of carriage returns (\\r) or run dos2unix immediately!\n" if (m/\r/);
in the loop where the SEQFILE is read.
Dear all,
I successfully tried protein_protein docking in PyRosetta before, but now I am trying to dock a RNA into a protein using the PyRosetta, which unfortunately fails ...
To run the docking I used the dna_dock.py script provided. When I run the script it finishes with following error message:
ERROR: unrecognized aa Ur
ERROR:: Exit from: src/core/io/pdb/file_data.cc line: 629
Traceback (most recent call last):
File "rna_dock.py", line 6, in
pose_from_pdb(p, "rnadock.pdb")
RuntimeError: unidentifiable C++ exception
hello
sorry to occupy your time.
I have run my openmp program in rosetta3.0.
such as add "fopenmp" into source/tools/build/basic.setting file.
and add "gomp" in apps.src.setting file,
but while I do the same thing in rosetta3.3,
I successfully compiled but my program still run in one thread.
so now I'm not sure the above change is right or wrong?
thanks for your help!
Hi,
when rescoring docked poses one obtains rather different scores. If I understand earlier posts correctly, the results from the 'score.xxx' application should be more suitable to distinguish the quality of docking results for different proteins than the docking score? (Please say yes ... ;-) Or would be 'relax.xxx' a better choice? I am trying to compare docking runs of slightly different peptides of identical length to the same target.
Hi,
I'm very new here. In fact, it is my first post. I'm a computer scientist which is studying protein structure prediction in ab initio modeling.
My doubt is concern about conversion of protein from dihedral angles representation to Cartesian representation. Where distances, angles and dihedrals of protein are stored? What algorithm is used for it?