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computer shuts down during autobulding with rosetta

i tried to run rosetta on a unix machine (ubuntu 9.04) for my data. Upto MR step everything goes fine , but during the rebuilding step after 20 cycles the computer shuts down.
i have attached the log file for the autobuilding run of rosetta. i am using phenix 1.7.1-743 version.

i will be grateful if some one helps me out

the error message is as folows

Parameters taken from: /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/PARAMS_1.eff

# mr_rosetta
# Run automr/autobuild/rosetta together

# Type phenix.doc for help

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(1) Score pose, (2) move atom, (3) score pose

from rosetta import *
import sys


pose = Pose()
scorefxn = create_score_function_ws_patch('standard','score12')

scorePose = scorefxn(pose)
print scorePose
coord = pose.residue(740).atom('N').xyz()
print coord
coord.x = 100.0
print coord
scorePose = scorefxn(pose)
print scorePose


core.pack.task: Packer task: initialize from command line()
core.scoring.dunbrack: Dunbrack library took 0.01 seconds to load from binary

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script "rebuild and refinement" sampling methodology for allosteric coupling

Similar to the Rosetta simulations done in Kidd, Baker,Thomas "Computation of Conformational Coupling in Allosteric Proteins", PLoS Computational Biology , 2009, 5(8), I would like to generate structure ensembles for allosteric regulated proteins using PyRosetta. Starting from crystal or homology structure with/without a bound allosteric effector molecule I want to generate new conformations to analyze the effect of different compounds.

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flexpepdock flag "-packing:unboundrot"

I'm running flexpepdock with the flag "-unboundrot" and getting this error when I set the -nstruct flag manually (versus using the default of 1).

>[path to rosetta]/FlexPepDocking.linuxgccrelease
-database [path to db]
-s input.pdb
-native native.pdb
-receptor_chain 'A'
-peptide_chain 'H'
-rep_ramp_cycles 2
-mute protocols.jd2.JobDistributor
-nstruct 1

ERROR: No values of the appropriate type specified for multi-valued option -packing:unboundrot

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rosetta 3.2.1 on mac os 10.6.8 - compiling problem

I am having trouble compiling rosetta. In the directory rosetta_source I ran varous "python mode=release [etc]" commands and ended up with various errors. Below I put three examples. I have installed the XCode tools and have gcc version 4.2. I don't want to install another version since seems to require other programs (gmp and mpfr) and I have run into problems compiling them.

>python mode=release bin -j2
src/apps/public/ sorry, unimplemented: 64-bit mode not compiled in

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AbinitioRelax with restraints/constraints

Hi all,

Is it possible to do fragment assembly using AbinitioRelax with harmonic distance restraints.

I tried running it with this command line:

AbinitioRelax.linuxgccrelease -database ~/rosetta_database
-in:file:fasta t000_.fasta -in:file:native native.pdb
-in:file:frag3 aat000_03_05.200_v1_3
-in:file:frag9 aat000_09_05.200_v1_3
-abinitio:relax -relax:fast
-abinitio::increase_cycles 10 -abinitio::rg_reweight 0.5 -abinitio::rsd_wt_helix 0.5 -abinitio::rsd_wt_loop 0.5
-use_filters true
-psipred_ss2 t000_.psipred_ss2
-out:file:silent beta1_zn_preds.out

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Error while compiling Rosetta 3.2. on Ubuntu 11.04 (AMD64)


I am trying to build Rosetta 3.2 on my ubuntu box through scon. After modifying the source in accordance with htt-DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.5 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_38_0 -I/usr/local/include -I/usr/include src/protocols/jd2/archive/
{standard input}: Assembler messages:
{standard input}:535948: Warning: end of file in string; '"' inserted
g++: Internal error: Killed (program cc1plus)
Please submit a full bug report.

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