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Minimization question

In a two domain protein, I randomize the phi and psi angles of the interdomain linker and then energy minimize, considering only repulsive VDW. Oddly, about one third of the time, the minimization step increases the energy. Possibly the minimization function is considering only the residues that are allowed to move, but that that score function is considering the entire system. If this is what is going on, it is not what I expect or want, I'd like the minimization function to consider the entire system. Below is the python script.

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Rosetta3.2.1-LAM-MPI Run-Problem-More than 2 processor Jobs

Hi All:

I am a new Rosetta user. I had just finished compiling parallel Rosetta (rosetta3.2.1/gcc-4.4.3/LAM-MPI-7.1.4)
and can run 2 processor jobs with no issues. But jobs fail for more than two processors (error message below).
Any help would be greatly appreciated.



Linux System:

Linux node2n29 2.6.32-29-server #58-Ubuntu SMP Fri Feb 11 21:06:51 UTC 2011 x86_64 GNU/Linux

Parallel version of Rosetta was compiled using GCC/LAM-MPI-7.1.4

Run Command (memory used was 8 GB)

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rosetta 3.2.1 installation on fedora core 6


I am getting the floowing errors after executing the "scons bin mode=release" command:-
scons: Reading SConscript files ...
svn: '.' is not a working copy

scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.
File "/usr/local/rosetta-3.2.1/rosetta_source/SConscript", line 40, in

scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.

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Problem with HETATM entries in PDB file


I am using FARNA module for RNA denovo structure prediction. Some of the PDB files contain HETATM entries like this :

HETATM 191 P CH A 10 6.803 -7.485 -7.145 1.00 0.00 P
HETATM 192 O1P CH A 10 7.379 -8.656 -7.843 1.00 0.00 O
HETATM 193 O2P CH A 10 6.942 -6.135 -7.736 1.00 0.00 O
HETATM 194 O5* CH A 10 5.232 -7.767 -6.901 1.00 0.00 O
HETATM 195 C5* CH A 10 4.807 -8.876 -6.102 1.00 0.00 C

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Questions about rosetta fragment library ranking and fragment conformation sampling algorithm

Hi, I have some questions about fragment library used for de novo folding and loop modeling.

From what I have read, the score for ranking fragment conformations in a library consists of two parts, which are from psi-blast results and secondary structure prediction results. My questions are:

1) When performing the psi-blast that contributes to the ranking of fragment conformations in a library at one position, does the psi-blast involve the whole protein sequence or just a local region around that position?

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Rosetta installation


i am trying to install rosette latest version in ubuntu 10.10.
i have installed scons and python as minimum requirmnets.
Now how to buld rosetta...

while i am running command like :

# scons

here i am getting error.

scons bin mode=release
scons bin
scons -h
scons -H

What to do next....
can anybody help me out?

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errors while running rosetta 3.1

I have two queries regarding ab initio structure prediction with cs-rosetta using rosetta-3.1:
a) For one of the runs while using the script default.out I get the error ERROR: did not find coordinates for all sequence positions for empty_tag
and only one pdb is generated. The program is still running though.

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Problem with Parallel installation of Rosetta3.2


I am trying to install the parallel version of Rosetta3.2 with the command, scons bin mode=release extras=mpi
However I am getting the following error:

scons: Building targets ...

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Remote access to Rosetta on Blue Gene or another HPC system?

Is there a parallel version of the Rosetta suite (for example, on Blue Gene) available to the general research community anywhere? My local supercomputer network (SHARCNET in Ontario, Canada) does not have Rosetta installed so I am wondering whether I can access it elsewhere? If not, are there instructions available for doing HPC installations?

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