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Connecting 2 Domains Via Non-Flexible Linker

Submitted by jurkm on Mon, 2011-09-05 06:10

Hello,

I originally posted my question regarding modeling of a multi-domain oligomer under a different thread. After getting a lot of useful answers and consulting Ingemar Andre off the list I am still facing one major problem.

The protein at hand consists of two domains A and B connected by a structured linker. Structural models for all three "parts" are available. How would one connect these to obtain a full-length model?

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Rosetta 3 - General

error in cluster running

Submitted by albumns on Mon, 2011-09-05 00:24

Hello, I am running the protein docking task in cluster, but failed. here is my related files:

------run.sh------

#!/bin/tcsh
#PBS -l walltime=180:00:00 nodes=2
#PBS -N Rosetta_Job
# Batch-submission script for OpenPBS system

module load rosetta

cd /home/users/test

mpiexec -np 32 /opt/rosetta/rosetta_latest/bin/docking_protocol.linuxgccrelease @flags > log &

------flags------

-in
-file
-s input.pdb
# the input file should have two single, complete chains A and B

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Rosetta 3 - General

pepspec aplication - segmentation fault

Submitted by tiagogomes89 on Fri, 2011-09-02 11:18

Hi,

Running pepspec application, in rosetta 3.3 (mac osx 10.6.7), gives me a segmentation fault. Any idea why this happens?

thank you

Tiago

Log:

core.init: command: ../../rosetta_source/bin/pepspec_anchor_dock.macosgccrelease -database /Users/tiago/software/rosetta/rosetta3.3/rosetta_database/ @dock.args
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=1393114305 seed_offset=0 real_seed=1393114305
core.init.random: RandomGenerator:init: Normal mode, seed=1393114305 RG_type=mt19937

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Rosetta 3 - General

Fe3p Heme Iron Unrecognized Despite Loading Hem Params

Submitted by vsjasion on Fri, 2011-09-02 10:37

Hi All,
I am new to computational biology in general, so bear with me if this question is rudimentary. I am trying to dock two heme proteins together. We have trouble-shot other issues but we can't seem to get this one. Here is what we do:

/usr/local/rosetta3.2.1/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/docking_protocol.default.linuxgccrelease
-database /usr/local/rosetta3.2.1/rosetta_database
-extra_res_cen /usr/local/rosetta3.2.1/rosetta_database/chemical/residue_type_sets/fa_standard/residue_types/heme/HEM.params

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Rosetta 3 - General

cluster input_score_filter

Submitted by lj269 on Thu, 2011-09-01 15:29

Hi,
I'm trying to cluster structures from a symmetry modeling run (silent file) using the -cluster:input_score_filter flag to exclude structures below a certain energy eg

-cluster:input_score_filter -1780.35

However, I can't seem to get cluster app to pay any attention to the flag, any ideas?

Is there any other way to cluster the top x scoring structures?
Thanks
L

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Rosetta 3 - General

how to realize a free bb design? PackMover=fixed bb!

Submitted by ast on Wed, 2011-08-31 09:41

Hi,

maybe somebody can give me a hint:
how do i realize a free backbone design approach in pyrosetta? As far as I understand the PackMover in PyRosetta is the equivalent to the FixedBackbone Design in Rosetta?! Is there something like a FREE backbone equivalent? At the moment I´m using a combination of the PackMover + freeBB-Minimization to have some degree of bb movement in the end... but I suppose it´s not the same.

Thanks for your help!

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PyRosetta - General

Modeling of a Multi-Domain Dimer

Submitted by jurkm on Mon, 2011-08-29 01:39

Hello,

After doing ab initio structure prediction on the individual domains of my target protein I was trying to assess the quaternary structure of the dimer using the SymDock protocol. The results I get are, firstly, never for a full-length protein and, secondly, the amino acid numbering is confused; trying to extract pdbs from the silent out file results in an error message (core.io.silent: ERROR: add_chain_ending() invalid chain ending 226
ERROR:: Exit from: src/core/io/silent/ProteinSilentStruct.tmpl.hh line: 671).

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Rosetta 3 - General

"unrecognized aa ACT"

Submitted by einew on Sat, 2011-08-27 14:58

We're trying to dock two proteins. One of them has a bound acetate ion. We created the centroid & full atom params files for the acetate, residue name ACT, using the params generation utility. We specified the location of the params files in the flags script using the -extra_res flags. The file locations are correct. We modified the flags file from one that ran sucessfully before, so we're pretty sure that's correct. Nonetheless, the docking run crashes quickly with the message "unrecognized aa ACT". Acetate does have a C=O and an OXT, which may be causing problems.

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Rosetta 3 - General

PyRosetta compilation errors: Mac with python 2.6.7 from macports

Submitted by greatm31 on Thu, 2011-08-25 15:06

I've been trying to install PyRosetta on my 64-bit Mac running Snow Leopard (10.6). I'm using the macports version of python (2.6.7) because that version is required for scipy and matplotlib. However, the pre-combiled binaries for PyRosetta do not work for this version of python. I get this error:


Fatal Python error: Interpreter not initialized (version mismatch?)

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PyRosetta - Build/Install

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