The problem hasn't been solved
Dear:
I would like to compile Rosetta with 'extras=mpi' option but failed. It always said the following:
sh: mpiCC: command not found
scons: *** [build/src/release/linux/2.6/64/x86/gcc/mpi/apps/public/AbinitioRelax.o] Error 127
I want to design the sequences of an enzyme. I am not sure which method should I use. I am thinking of 2 methods:
1. Use fixbb and fix the enzyme site of the protein. just design the other part of the protein
2. Use Enzyme Design of rosetta 3.3. But this program seems only design the active sites.
Do you have any ideas? Thank you very much!
Hi,
I use Rosett_3.3 to design a protein whose length is 166. And the command is
fixbb.linuxgccrelease -s protein.pdb -resfile protein.resfile -ex1 -ex2 -nstruct 1 -database $ROSETTA_DATABASE -jran 111111 -fast_sc_moves True
However, it takes me more than 2 hour to finish the job. I use rosetta 2.3 to design the same protein with the same parameter. It takes me only 1-2 minutes.
Could you please tell me what parameters should I use to make the program fast?
I am trying to get Rosetta to work with Phenix phenix-1.7.3-928. But first I need to
get rosetta compiled. It does not compile without an error.I start with:
[rosetta@paprika ~/Desktop]$ python -V
Python 2.6.6
python scons.py bin mode=release
and it runs for a while and then:
I am using the kinetic loop refinement protocol these days. Since my protein is large than 300aa and the loop is over 20 aa. So it is really time comsuming even I use 24 CPU to run the jobs. It only generate 1 model after one hour.... I am planning to generate 5000 loop models. Is it possible to generate the loop model with hydrogen? At least without hydrogen for the no loop region?
THX
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
