# Unsolved

The problem hasn't been solved

## errors while running rosetta 3.1

Hi
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 extract_pdb3.com default.out I get the error core.io.silent: ERROR: did not find coordinates for all sequence positions for empty_tag
and only one pdb is generated. The program is still running though.

Post Situation:

## Problem with Parallel installation of Rosetta3.2

Hi ALL,

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 ...

Post Situation:

## 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?

Post Situation:

## Rosetta-Holes Scoring Function

I have been trying to use the scoring function to calculate the rosetta-holes score for a pdb file (Initially I am using the pdb provided in the scoring demo). I keep getting an error related to reading the input file. I think this is the input that is passed to DAlphaBall, but it might be some other problem I am unaware of. I am using the following command:
 score_jd2.linuxgccrelease -s test_in.pdb -score:weights holesscore -database ../../../rosetta_database/ -holes:dalphaball "pathToDAlphaBallExe"
and I get the following error (repeated for 10 tries):

Post Situation:

## Parallel installation of Rosetta3.2 with MPI

Hi ALL,

I want to install a parallel version of Rosetta3.2 (Abinitiorelax / relax etc.) using MPI. I find some people have already done so and using it. Can someone please tell me the steps/options with which I need to install the parallel version of Rosetta3.2.

Regards,

Anirban

Post Situation:

## install rosetta problems

Hi,
I am trying install rosetta on the fedora system,with gcc 4.1.2 and scons 2.0.1. But I encountered a problem while I install with the command:scons bin mode=release.
there are two warnings that always repeat again and again, I do not know how to solve this problem.
scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.
File "/xtal_programs/rosetta3.2.1/rosetta_source/SConscript", line 40, in

scons: warning: No hashlib or MD5 module available, CacheDir() not supported

Post Situation:

## ddg Script Problem

Hi guys. I'm trying to use the ddg script from Sid on an interface, and after changing the DockingProtocol().setup_foldtree to DockingProtocol().set_autofoldtree,
I'm now getting an undefined error for the Interface(dock_jump) step. Is there an equivalent name in 2.0?

-J

Post Situation:

## Pyrosetta 2.0 - Dunbrak library binary not loading - strange repacking score

All,

I am getting large energy increases when repacking a protein using v2.0 of PyRosetta.ScientificLinux64bit (I'm running RHEL5.5_64, Python 2.66)

1st issue On init(), I recieve:

 basic.io.database: Database file opened: .../minirosetta_database/Rama_smooth_dyn.dat_ss_6.4 core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 7533 residue types core.pack.task: Packer task: initialize from command line() Warning: Unable to locate database file Dunbrack02.lib.bin

Post Situation:

## Generate structural fragments

Hello everyone,when I run "/rosetta/fragments/nnmake/make_fragments.pl -nopsipred -nosam -nojufo -noprof -verbose trhl2.fasta",I got the error follow:
[root@localhost input]# /rosetta/fragments/nnmake/make_fragments.pl -nopsipred -nosam -nojufo -noprof -verbose trhl2.fasta
Run options:
be verbose.
don't run psipred.
don't run prof.
don't run jufo.
don't run sam.
FILENAME: trhl2.fasta
no id specified. parse filename instead.
INTERMEDIATE: trhl2.fasta
ID: trhl CHAIN: 2
Warning: can't find executable file /work/chu/src/shareware/psipred/bin/psipred!

Post Situation:

## Dunbrack Library

Hi All;

I'm trying to import a new Dunbrack library into PyRosetta.
I've found the RotamerLibrary class in core.pack.dunbrack._dunbrack_all_at_once and a method create_fa_dunbrack_libraries(), but I am unsure how to call it or setup an instance. Can anyone help? Thanks.

-Jared

Post Situation: