You are here

Solved

The problem has been solved

Rosetta3.3 installation error

Dear developers,

I have downloaded Rosetta3.3 and run Scons bin mode=release. Everything seemed to be fine till I ran the tenzyme_design protocol.

Here is what I got:

/usr/local/rosetta3.3/rosetta_source/bin/enzyme_design.linuxgccrelease -database /usr/local/rosetta3.3/rosetta_database/ @flags >first_try.log

/usr/local/rosetta3.3/rosetta_source/bin/enzyme_design.linuxgccrelease: error while loading shared libraries: libprotocols.so: cannot open shared object file: No such file or directory

I can find the liprprotocols.so file in one of the directories:

Post Situation: 

How to get PyRosetta on OS X 10.6.6 working successfully

Hello all,

I thought I would post this here to help other folks installing PyRosetta.

My system is as follows:
OS X 10.6.7
Intel Core 2 Duo - 64 bit (To find out if you have a 64 bit machine go here http://support.apple.com/kb/ht3696)
X-Code installed
Native OSX python

1) After you have installed X-code and download PyRosetta open up your terminal and type:
$ which python

You should see something like this:
/usr/bin/python

Then at the command line type:
$python

Your output should look like this:

Python 2.6.1 (r261:67515, Jun 24 2010, 21:47:49)

Post Situation: 

Scoring issues - differs from command line vs .py file - for a simple ddG loop

Hello all,

I was able to get PyRosetta up and running on my mac under OS X 10.6.6 . I am working on what I think is a simpler version of the ddG script (we don't need the docking feature). What I am trying to do is bring in a pdb file, score it using the ddG paramters, and then mutate each residue (basically cycle through all the possible combinations)to see what happens to the ddG values are. The start of the script is here: (The loop is a mess at the moment)

from rosetta import *
init()

pose = Pose()
pose_from_pdb( pose , "2O2X_clean.pdb" )

pymover = PyMOL_Mover()

Post Situation: 

prepack_example.sh error message

Dear all,

I am running pre pack_example.sh while using FlexPepDocking. I have used almost the same commands and flags as what I have used in the example 2b1z (where 2b1z runs fine) on a new antibody-peptide pair, 2hfg, but I got the following error while running

FlexPepDocking.linuxgccrelease -database $PATH_TO_DB @../prepack_flags. Could someone point out what have I done wrong please?

Error message:

ERROR: this_pose.total_residue() == residue_packstat_.size()
ERROR:: Exit from: src/protocols/toolbox/pose_metric_calculators/PackstatCalculator.cc line: 164

Post Situation: 

null rosetta energy/score

Hi there,
I have extracted the 5% best scores structure from 100,000+ decoys and combine them into one single silent file. After clustering I have realized their rosetta energy/score are all null. Of course, I was intend to cluster and sort them by energy. However, the score flag have been lost upon extract process. Is there any keyword to preserve their energy flags when extracting?

Post Situation: 

error: CPU you selected does not support x86-64 instruction set [SOLVED]

Dear colleagues,

I am trying to install Rosetta 3.3 on:

- HP ProLiant DL380 G6
- CPU: 2 x Intel Xeon Quad Core
- OS = SUSE SLES 11, kernel 2.6.27.19, x86_64
- compiler: gcc 4.3-62.198-x86_64
- python: 2.6.5
- scons: 2.1.0

command: scons bin mode=release OR additionally arch=x86 arch_size=64

crash + error message:

Post Situation: 

Debugging Rosetta under XCode

Hi all,

I am new in Rosetta. I am planning to add a new empirical force field to rosetta, but I have no idea what is the best cutting point in order to be able to debug it. Here is my question.....
1. What's the size of the memory typically required for debugging Rosetta under Xcode?

The configuration of my machine:

Processor 2.8 GHz Intel Core 2 Duo
Memory 8 GB 1067 MHz DDR3
Software Mac OS X Lion 10.7.2 (11C74)

I have successfully compiled Rosetta using "-j 2 mode=debug bin --". The default compiler is GCC 4.2.

Post Situation: 

Rosetta numbering with missing occupancies

Hi,

I've a short question so it should only require a short answer :-).

How does Rosetta numbering work with missing occupancies? For example, say we have a PDB structure containing three residues A6, A7, and A8. If all atoms of the second residue A7 have zero occupancy, does Rosetta map A6 to residue 1 and A8 to residue 2, omitting A7?

Post Situation: 

minimize_with_cst problems (ddg_monomer)

Hi all,

I'm trying to use the ddg_monomer application as described in the rosetta3.3 manual. It gives a command for preminimization of your input pdb structure using the application "minimize_with_cst". Trying this exact code with my pdb, or even with 2ci2.pdb found with the integration test, ends with "using -l option" as the last line of the output. Anyone else having similar problems or have a solution?

Post Situation: 

Pages

Subscribe to RSS - Solved