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Compilation

How to read the output score file from rosetta?

Category: 
Compilation

Dear all, 

I find the score file output by rosetta is different to read. For example, a score-snugdock.sf file produced by snugdock reads like the following in gedit:

https://www.dropbox.com/s/6oba8nitiwob7pb/score.PNG?dl=0

I cannot tell the column names and their corresponding values. The Rosetta documnet gives a sort command that can pick out the structure with the lowest score:

 sort -nk5 score-snugdock.sf | head -n1 | awk '{print $NF}'

Post Situation: 

libmpc.so.2: cannot open shared object file

Category: 
Compilation

I am attempting to install Rosetta/3.8 on a Linux Cluster running Redhat 5.6. I am compiling with gcc/4.9.3 and mpich 3.2. I have come across the following error:

/exports/apps/gcc/4.9.3/libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/cc1plus: error while loading shared libraries: libmpc.so.2: cannot open shared object file: No such file or directory

Post Situation: 

Running snugdock was crashed by "segmentation fault"

Category: 
Compilation

Hello everyone,

When using the following command to run snugdock in my centos 7 system:

 snugdock.linuxgccrelease -s antibody_antigen_start.prepack_new.pdb \
     -ensemble1 antibody_ensemble.list \
    -ensemble2 antigen_ensemble.list \
    -detect_disulf false \
    -antibody:auto_generate_kink_constraint \
    -antibody:all_atom_mode_kink_constraint \
    -nstruct 20 \
   -multiple_processes_writing_to_one_directory > snugdock.log 2>&1 &

Post Situation: 

The problems on pdb renumbering

Category: 
Compilation

Hello everyone,

I am learning to do antibody-antigen docking with snugdock. The antigen I am working on has two chains (chain A and B). Before the antigen pdb file can be used for docking, it must be renumbered (changing it to a single A chain and numbering all residues continuously), am I right? There is some renumbering scripts in the Rosetta package. I have tried some of them, but none can work. 

(1)  The pdb_renumber.py script in the /app/rosetta_src_2017.08.59291_bundle/tools/protein_tools/scripts directory. The command:

Post Situation: 

Cannot run binaries after successful compilation

Category: 
Compilation

Dear all,

I have been trying to compile rosetta 3.8 for a while now without success (meathod worked will with 3.7). I have a 17.04 Ubuntu Gnome Operating System.

Compile Commands:

sudo apt install zlib1g-dev scons build-essential -y
tar -xvzf rosetta_src_3.8_bundle.tgz
cd {ROSETTA}/main/source
./scons.py mode=release bin

 

Result:

Successfully compiles everything, no errors printed.

 

Post Situation: 

How to set the enviroment variable $ROSETTA3, $ $ROSETTA3_DB, $ROSETTA_TOOLS?

Category: 
Compilation

Dear all,

The "How To Read These Tutorials" section (https://www.rosettacommons.org/demos/latest/tutorials/How_To_Read_These_Tutorials/Tutorial_Setup) of the tutorial of Rosetta  requires the following environment variables are set: 

 

env $ROSETTA3=the path to your Rosetta/source directory

Post Situation: 

Error running unit test executable

Category: 
Compilation

Hello!

I was trying to test my Rosetta installation and at the begining of test I've got an error:

I didn't find any solution on Rosetta Forum. 

server@localhost:~$ python test/run.py
Identifying platform...

Platform found: debug/linux/4.10/64/x86/gcc/6.3/default
Error running unit test executable for protocols.test - not all tests may be availible.

Error running unit test executable for core.test - not all tests may be availible.

Post Situation: 

build rosetta3 with gpu support failed

Category: 
Compilation

I tried to install rosetta3 with gpu support with the follow command: 

 sudo ./scons.py -j 20 mode=release bin extras=opencl

but failed with the follow error message:

scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/opencl/protocols/hotspot_hashing/SurfaceSearchPattern.os] Error 1
scons: building terminated because of errors.

My system is centos7 implemented with 2 c2050 gpu, and cuda-8.0 has been installed in the system. Why does the error occurs? Is there some way to solve this problem?

Post Situation: 

build error in linux-centos

Category: 
Compilation

Hello everyone!

 I recently upgraded to CentOS7. So, I had to do a fresh installation of Rosetta. I am trying to build the latest version of rosetta with this command:-

$ sudo ./scons.py -j10 bin mode=release extras=static

The building terminates with an error like this:-

I think the same type of error is popping up while trying to compile different applications. Could someone help me with this?

Post Situation: 

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