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Creation of core.* file in current running directory

Submitted by alejandro on Tue, 2011-12-06 06:19

Good afternoon,

I'm using Rosetta as a library inside my own code and I'm running several instances of my programs on a cluster. It happens that, sometimes, a file named core.* is created in the directory where the programs are launched where * is a number (e.g. 1041, 15897, etc.). This file can weight up to 2GB but its size varies.

Can anyone explain this behavior, tell me if it's normal and give me some clues to avoid the creation of this file?

Thank you in advance for your help

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Rosetta 3 - General

Rosetta 3.3 installation error

Submitted by bharat_46010 on Tue, 2011-12-06 04:20

Hi,

I am trying to install rosetta 3.3 on fedora core 14 platform. I am getting the following error after executing scons bin mode=release command :-

[pauling@BME rosetta_source]$ scons bin mode=release
scons: Reading SConscript files ...
Traceback (most recent call last):
File "/home/pauling/Downloads/rosetta3.3_bundles/rosetta_source/SConstruct", line 139, in main
build = SConscript("tools/build/setup.py")
File "/usr/lib/scons/SCons/Script/SConscript.py", line 614, in __call__
return method(*args, **kw)

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Rosetta 3 - Build/Install

ddg with ligands

Submitted by bhaines1 on Mon, 2011-12-05 14:32

Could someone please recommend a way to include ligands in a ddg calculation (using ddg_monomer or otherwise)? I'd like to estimate the effect of mutations to the protein domain on the stability of the interface between said protein domain and the enzyme substrates.

Thank you in advance for any response!
Brandon

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Rosetta 3 - Applications

problems in InterfaceAnalyzer analysis

Submitted by chenchaozhao on Fri, 2011-12-02 23:36

Hi, everyone!

Now I met a samll bug during InterfaceAnalyzer analysis as follows.

`core.io.silent: Reading all structures from 1-46wt.out
core.io.silent: bad format in sequence line of silent file
core.io.silent: line = SEQUENCE:
core.io.silent: tag = SEQUENCE:
terminate called after throwing an instance of 'utility::excn::EXCN_BadInput'

And the starting lines of my silent file are:
`SEQUENCE:

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Rosetta 3 - Applications

Can one use a non-write privileged rosetta executable?

Submitted by jhbrown on Tue, 2011-11-29 12:15

I am trying to do a comparative modelling using /sware/rosetta3.3/linux/rosetta_source/bin/minirosetta.linuxgccrelease.
The program didn't run, and the last few lines of the log file are:

Warning: Unable to locate database file Dunbrack02.lib.bin
core.pack.dunbrack: Dunbrack library took 8.4 seconds to load from ASCII
Warning: Unable to locate database file Dunbrack02.lib.bin
Warning: Unable to locate database file Dunbrack02.lib.bin
core.pack.dunbrack: Opening file /sware/rosetta3.3/linux/rosetta_database/dun02bwtPgW for output.

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Rosetta 3 - Build/Install

Representing Cross-linked nitrogens

Submitted by jjlee2 on Sat, 2011-11-26 18:42

I am trying to use Rosetta 3.3's Ab-initio relax program to fold a protein with cross-linked lysines. I am trying to use distance constraints to represent the cross links, but every time I try to run Ab-initio on the following constraint file, I get the error "Exception : Atom NZ 26 not found". Does anyone know why this might be happening?

Thanks

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Rosetta 3 - Applications

Energy calculation for protein design

Submitted by Filipe on Sat, 2011-11-26 15:01

Hi,
I'm doing my thesis about Protein Design using a ASP solver. My area is Informatic, so i don't understand many things about proteins.
For my work i have a fixed backbone and i have to do a asp program that determine the optimum set of rotamers for that backbone.
I need to have a energy table with all energies for all possible rotamers.
I think that rosetta might help me, but i can't exactly figure it out how i do it.
I've already installed rosetta.

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Rosetta 3 - General

Runnig Abinitio & score app

Submitted by Gaurav_kumar on Wed, 2011-11-23 20:45

I am new user of rosetta and still trying to figure out the commands and its function. I have installed rosetta3.3 on my suse 11.3 and now try to run the abintio application.The problem im facing is that i am not able to either pass on the flags/options in the command or may be doing it in incorrect manner.
Can anyone help me to run two programs 1.AbinitioRelax.linuxgccrelease for which i used %(bin)s/minirosetta.%(binext)s @flags -database %(database)s -run:constant_seed -nodelay 2>&1 \ protocol
The command goes like this:

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Rosetta 3 - Applications

Don't know how to extract scores from a RNA de novo silent file.

Submitted by Basantab on Wed, 2011-11-23 17:27

Hi,

I have a silent file containing the structures from a RNA de novo run. I have been able to extract the pdbs using the rna_extract application, but I'm unable to extract scorefiles, no matter what flags I use, it just extracts the PDB files with no scores in them. I would like to know which is the right application/flag to use, or if there's any simple console command to get the structures in an order according to increasing total energy.

So far I have tried:
rna_extract.exe -out:file:scores_only -database ./rosetta_database -in:file:silent myfile.silent

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