The problem hasn't been solved
Could someone please clarify the examples of angle constraints mentioned here:
http://www.rosettacommons.org/manuals/archive/rosetta3.2.1_user_guide/co...
Specifically, in the example below, is 1.95 in radians or degrees?
Angle CB 5 SG 5 ZN 32 HARMONIC 1.95 0.35
Hi
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
I'm am unsure of how to do this. AtomID() does not fit any of the standard types in __init__.Vector1().
For a double, you can do:
vec1 = rosetta.utility.vector1_double()
vec1.append(doubleX)
from rosetta import *
import sys
init()
pose = Pose()
scorefxn = create_score_function_ws_patch('standard','score12')
pose_from_pdb(pose,'config.pdb')
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
Returns:
...
core.pack.task: Packer task: initialize from command line()
core.scoring.dunbrack: Dunbrack library took 0.01 seconds to load from binary
-1347.47520146
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.
i have been trying to install rosetta on ubuntu 9.04 but has some problems.
the few last lines appear as follows
sh: o: not found
sh: o: not found
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'
-rbMCM
-torsionsMCM
-rep_ramp_cycles 2
-ex1
-ex2aro
-mute core.io.database
-mute core.util.prof
-mute protocols.jd2.JobDistributor
-unboundrot
-nstruct 1
ERROR: No values of the appropriate type specified for multi-valued option -packing:unboundrot
I am having trouble compiling rosetta. In the directory rosetta_source I ran varous "python scons.py 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 scons.py mode=release bin -j2
src/apps/public/AbinitioRelax.cc:1: sorry, unimplemented: 64-bit mode not compiled in
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
Hi,
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/ArchiveManager.cc
{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.
