Unsolved

Hello all,
I try to build reosetta on a mac os 10.8.5 to use Erraser within Phenix 1.8.4-1496.
When I type
benoit1$ python external/scons-local/scons.py -j2 bin mode=release
Verbose gives
scons: Reading SConscript files ...
Running versioning script ... Done. (0.0 seconds)
scons: done reading SConscript files.
scons: Building targets ...

I newly start Rosetta for rna structure prediction. I know that rna_denovo is not suitable for large RNAs. but i tried an approximate 150nt RNA fasta which resulted in structures without any watson crick base pairs! Then I tried the same fasta with a homolog pdb with below command which led to an error after half an hour with one cpu.

./bin/rna_denovo.default.linuxgccrelease -fasta lysine.fasta -native lysine_RNA.pdb -nstruct 2 -out::file::silent lysine2.out -cycles 1000 -minimize_rna -database /opt/rosetta/rosetta_database

I am working on ab initio folding of a dimeric molecule using distance constraints.
The constraints format being used is similar to NMR derived NOE constraints.
But, data is not derived from NMR.
I was wondering if that is the correct way to impose constraints on any general
system.

Flagfile:
~/rosetta. -seed_offset `echo $RANDOM` -cst ~/test.cst -cst_min -nstruct 10000
-paths ~/paths.txt -output_pdb_gz -timer -fa_output -output_silent_gz
-read_all_chains -randomize1 -symm_type cn -pose_fold_and_dock
-docking_pose_symmetry -pose1 -slide_contact_frequency 0.01

Hello,

Recently I developed rigid body minimization algorithm and then extend it to also consider torsional flexibility. Here is the list of the papers:

Rigid Body Energy Minimization on Manifolds for Molecular Docking
http://pubs.acs.org/doi/abs/10.1021/ct300272j

A new Approach to Rigid Body Minimization with Application to Molecular Docking
http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6426267

Flexible Refinement of Protein-Ligand Docking on Manifolds
http://www.nt.ntnu.no/users/skoge/prost/proceedings/cdc-2013/media/files...