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script "rebuild and refinement" sampling methodology for allosteric coupling

Submitted by Stefan on Thu, 2011-07-14 09:27

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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PyRosetta - Scripts

flexpepdock flag "-packing:unboundrot"

Submitted by gw on Mon, 2011-07-11 12:23

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

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Rosetta 3 - Applications

rosetta 3.2.1 on mac os 10.6.8 - compiling problem

Submitted by gw on Mon, 2011-07-11 10:48

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

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Rosetta 3 - Build/Install

AbinitioRelax with restraints/constraints

Submitted by jtmacd on Mon, 2011-07-11 07:07

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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Rosetta 3 - General

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

Submitted by jkrellenstein on Wed, 2011-07-06 08:47

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.

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Rosetta 3 - Build/Install

error while loading shared libraries: libdevel.so

Submitted by jarek on Wed, 2011-07-06 03:11

I have successfully built rosetta 3.2.1 on fedora14, but
now whenever I try to execute any of the programs I get the following message:
error while loading shared libraries: libdevel.so: cannot open shared object file: No such file or directory

Do I need to set up some path variables? I haven't found any info in the manual.

Thanks for your help,

Jarek

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Rosetta 3 - Build/Install

How to define pi-pi stacking in cst file?

Submitted by lzx32 on Mon, 2011-07-04 23:47

Dear developers,

In the design of the kemp enzyme, a pseudoatom (X1) that represents the aromatic moeity was introduced to define the pi-pi stacking between an aromatic residue and the ligand. The block from the cst file is shown here:

#block 5 for aromatic binding

CST::BEGIN
TEMPLATE:: ATOM_MAP: 1 atom_name: X1 C10 C12
TEMPLATE:: ATOM_MAP: 1 residue3: D2N

TEMPLATE:: ATOM_MAP: 2 atom_type: aroC,
TEMPLATE:: ATOM_MAP: 2 residue1: WFY

CONSTRAINT:: distanceAB: 3.50 0.20 50.00 0
CONSTRAINT:: angle_A: 90.00 5.00 50.00 360.00

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Rosetta 3 - Applications

Compiling Rosetta 3.2 on Mac OS X using scons

Submitted by nkemjika on Thu, 2011-06-30 00:19

hi & thanks in advance,

preamble:

Mac OS X version: 10.6.8 | # Processors: 1
Rosetta version: 3.2
scons version: 2.1.0.alpha.20101125
Xcode version: 3.2.6
UNIX Shell: bash

problem:

i'm having difficulties compiling Rosetta with scons.
so far, i have followed the steps on the rosetta user guide page (at: (http://www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide/)) to no avail.

first i installed scons without administrative privileges using the command:

$ python setup.py install --prefix=$HOME

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Rosetta 3 - Build/Install

rosetta 2.1.1- Installation problems in mac os x 10.6

Submitted by cctristan on Tue, 2011-06-28 11:33

Hi all, I have to install rosetta 2.1.1 since some code has been modified in this version by ourselves for special use two years ago. Now I have a problem about the installation.

I have successfully built rosetta 2.1.1 in Redhat by
$ make gcc64

the gcc version is :
gcc (GCC) 4.1.2 20070626 (Red Hat 4.1.2-14)
Copyright (C) 2006 Free Software Foundation, Inc.

However when I tried to build it in mac os x 10.6, I came across some errors.

In mac os x 10.6.8,

gcc version:
i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3)

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Rosetta++ - Build/Install

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