RosettaCommons - Rosetta++ - Build/Install

READ ME FIRST

rmoretti — Fri, 04 Sep 2015 22:24:56 +0000

This is a forum dedicated to Rosetta++.

Development of Rosetta++ (aka Rosetta2) ceased around 2010.

The current version of Rosetta is Rosetta3. -- Please see the Rosetta3 forums for help on using Rosetta3.

Access and support to Rosetta++ is provided primarily for recapitulation of previous results. It is highly recommended that all new projects use Rosetta3 rather than Rosetta++.

We will attempt to help you as much as possible with Rosetta++, but please be advised that Rosetta++ is no longer in frequent use.

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Compilation

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Rosetta++ - Build/Install

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Problems to install rosetta rosetta_bin_linux_2021.07.61567_bundle

rtorquato — Wed, 23 Jun 2021 01:05:25 +0000

Hi, can some body help me.

I got this message, after use the command: ./scons.py -j22 bin mode=release extras=mpi

build/src/release/linux/4.15/64/x86/gcc/7/mpi/libprotocols.3.so: undefined reference to `ompi_mpi_float'
build/src/release/linux/4.15/64/x86/gcc/7/mpi/libprotocols.4.so: undefined reference to `ompi_mpi_char'
build/src/release/linux/4.15/64/x86/gcc/7/mpi/libprotocols.1.so: undefined reference to `ompi_mpi_group_null'
build/src/release/linux/4.15/64/x86/gcc/7/mpi/libprotocols.4.so: undefined reference to `ompi_mpi_int'
build/src/release/linux/4.15/64/x86/gcc/7/mpi/libprotocols.3.so: undefined reference to `ompi_mpi_double'
build/src/release/linux/4.15/64/x86/gcc/7/mpi/libprotocols.4.so: undefined reference to `ompi_mpi_comm_world'
build/src/release/linux/4.15/64/x86/gcc/7/mpi/libprotocols.3.so: undefined reference to `ompi_mpi_op_sum'
build/src/release/linux/4.15/64/x86/gcc/7/mpi/libprotocols.3.so: undefined reference to `ompi_mpi_comm_null'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/4.15/64/x86/gcc/7/mpi/UBQ_Gp_CYD-CYD.mpi.linuxgccrelease] Error 1
scons: building terminated because of errors.

All the best

Ricardo

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Compilation

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Rosetta++ - Build/Install

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Problems with Installing and Running MR Rosetta 3.10

Priscilla Masamba — Sun, 18 Aug 2019 21:15:48 +0000

I am having a serious challenge running MR Rosetta3.10. Everytime i run it, an error written "sub-process failed" pops up and when i check the log file it indicates that it is looking for a particular file eg score3.wts. Once i get that file linked and run it again, the same error pops up again looking for another set of files e.g ncaa.rotamer.libraries which i do have. This has happened three times with different file searched and it is quite monotonous because my runs take over 18 hours only to receive error messages at the end of the day. My computer technician has told me that it seems like the database is not linked or meged with the Rosetta3.10 source code. How can this problem be fixed? Please do assist...

Priscilla

Category:

Phenix / MR Rosetta

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Rosetta 3 - Build/Install

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Installing rna_denovo

Tanusree Chaudhuri — Fri, 26 Apr 2019 06:59:52 +0000

Hi,

I tried using the Rosetta RNA tertiary structure modeling pipeline as described in your article "Modeling complex RNA tertiary folds with Rosetta."

My build is correct.

But every time I try to run

helix_preassemble_setup.py -secstruct sec.txt -fasta fasta.fasta

I am getting error as

subprocess.check_call([str(elem) for elem in cmdline.split()])
File "/usr/lib/python2.7/subprocess.py", line 185, in check_call
    retcode = call(*popenargs, **kwargs)
File "/usr/lib/python2.7/subprocess.py", line 172, in call
    return Popen(*popenargs, **kwargs).wait()
File "/usr/lib/python2.7/subprocess.py", line 394, in __init__
    errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1047, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory

going back to the code, in line 75,

"rna_denovo -score:weights stepwise/rna/rna_res_level_energy4.wts -minimize_rna true -use_legacy_job_distributor true -restore_talaris_behavior true "

this rna_denovo is called.

But, in rosetta bin there is no .exe called rna_denovo, instead I found,

rna_denovo.default.linuxgccrelease
rna_denovo.linuxgccrelease
rna_denovo.static.linuxgccrelease

not sure, why is name mismatch and how to call rna_denovo.

So my pipeline is not working.

Can you help me resolving this issue?

Thanks,

Tanusree

Category:

Nucleic Acids

Forums:

Rosetta++ - Build/Install

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ss DNA 3D Model Structure Building

irshadbaig — Mon, 18 Nov 2013 04:13:15 +0000

Dear Sir,
Hello!. I am Irshad Baig, pursuing PhD in Biochemistry.

I am writing you to seek your help regarding 3D structure prediction of ss DNA and ssDNA-Protein docking studies.

Infact, I am trying to build 3D model structure for my ss DNA aptamer, as i am further interested to study DNA -protein interaction through docking. However, I did not succeed in building 3D struture for ss DNA aptamer.

Trying one reccommended programme,i could able to built 3 D model for ss DNA,however it is in the 'B' form of DNA,however i need 3 D model of ss DNA in the native stem/loop form. Further, I have predicted secondary structures of my ssDNA aptamers by Mfold programme, however I did not find any modeling programme to predict tertiary (3D) structure of a DNA, thus would generate PDB/PDBQT file of the DNA aptamers that would be further helpful to study DNA-Protein docking, i assume.

Therefore, I would highly appreciate, if you could please extend me your valuable guidance/suggestions to perform 3D structure prediction of ss DNA aptamer and ss DNA aptamer-Protein docking.

Should you need any information, please do let me know.

Looking forward for your kind suggestions to resolve this issue.

Thank you,

Sincerely,
Irshad Baig
irshad@hanyang.ac.kr

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Rosetta++ - Build/Install

ss DNA 3D Model Structure Building

irshadbaig — Mon, 18 Nov 2013 04:13:12 +0000

Dear Sir,
Hello!. I am Irshad Baig, pursuing PhD in Biochemistry.

I am writing you to seek your help regarding 3D structure prediction of ss DNA and ssDNA-Protein docking studies.

Infact, I am trying to build 3D model structure for my ss DNA aptamer, as i am further interested to study DNA -protein interaction through docking. However I did not succeed in building 3D struture for ss DNA aptamer.

Therefore, I would highly appreciate, if you could please extend me your valuable guidance/suggestions to perform 3D structure prediction of ss DNA aptamer and ss DNA aptamer-Protein docking.

Should you need any information, please do let me know.

Looking forward for your kind suggestions to resolve this issue.

Thank you,

Sincerely,
Irshad Baig
irshad@hanyang.ac.kr

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Rosetta++ - Build/Install

error with profit

jchin — Thu, 15 Nov 2012 18:00:44 +0000

Hi,

I get an error below with profit being called on profit.in

Scan one or more sequences with a simple frequency matrix
Profile or weight matrix file: Error: Unable to open file 'QUIET' for input
Profile or weight matrix file: Error: Unable to open file 'ZONE CLEAR' for input
Died: profit terminated: Bad value for '-infile' and no more retries
256 at /home/.../immunity/antibody/scripts/ram_buildloop_wrapper4.pl line 12

The contents of profit.in (below), don't seem to match the expected input for profit.

QUIET
ZONE CLEAR
ATOMS CA
templatelightheavy.pdb queryL.pdb
reference templatelightheavy.pdb
mobile queryL.pdb
ZONE L4-L6
ZONE L10-L23
ZONE L35-L38
ZONE L45-L49
ZONE L57-L66
ZONE L71-L88
ZONE L98-L104
fit
WRITE queryLfitted.pdb
--
Thanks!

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Rosetta++ - Build/Install

some "COMMAND ERROR" while installing rosetta2.1.0

sdg_lab — Thu, 22 Mar 2012 05:57:09 +0000

I am trying to install Rosetta++2.1.0
and I changed the options.settings file to be compatible with gccc 4.5 which is in my my CYGWIN
but I am getting the following big error.

I will be very grateful if somebody could suggest a solution:

ERROR :
cygwin warning:
MS-DOS style path detected: C:\Documents and Settings\All Users\Application Da ta\scons/site_scons
Preferred POSIX equivalent is: /cygdrive/c/Documents and Settings/All Users/Ap plication Data/scons/site_scons
CYGWIN environment variable option "nodosfilewarning" turns off this warning.
Consult the user's guide for more details about POSIX paths:
http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
scons: Reading SConscript files ...

scons: warning: The Options class is deprecated; use the Variables class instead .
File "/home/user/rosetta/rosetta++/tools/build/setup.py", line 32,in setup_build_options
scons: warning: The EnumOption() function is deprecated; use the EnumVariable() function instead.
File "/home/user/rosetta/rosetta++/tools/build/setup.py", line 40, in setup_build_options

scons: warning: The ListOption() function is deprecated; use the ListVariable() function instead.
File "/home/user/rosetta/rosetta++/tools/build/setup.py", line 48, in setup_build_options

scons: warning: The build_dir keyword has been deprecated; use the variant_dir k eyword instead.
File "/home/user/rosetta/rosetta++/SConscript", line 19, in

scons: warning: The env.Copy() method is deprecated; use the env.Clone() method instead.
File "/home/user/rosetta/rosetta++/src/SConscript.src", line 86, in

scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.
File "/home/user/rosetta/rosetta++/SConscript", line 19, in

scons: warning: The build_dir keyword has been deprecated; use the variant_dir k eyword instead.
File "/home/user/rosetta/rosetta++/SConscript", line 19, in

scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.
File "/home/user/rosetta/rosetta++/SConscript.rosetta++", line 20, in
Traceback (most recent call last):
File "/home/user/rosetta/rosetta++/SConstruct", line 101, in main
SConscript("SConscript.rosetta++", "build")
File "/usr/lib/scons-2.1.0/SCons/Script/SConscript.py", line 614, in __call__
return method(*args, **kw)
File "/usr/lib/scons-2.1.0/SCons/Script/SConscript.py", line 551, in SConscrip t
return _SConscript(self.fs,**subst_kw) *files,
File "/usr/lib/scons-2.1.0/SCons/Script/SConscript.py", line 260, in _SConscri pt
exec _file_ in call_stack[-1].globals
File "/home/user/rosetta/rosetta++/SConscript.rosetta++", line 20, in
build_dir = build_path, duplicate = False)
File "/usr/lib/scons-2.1.0/SCons/Script/SConscript.py", line 614, in __call__
return method(*args, **kw)
File "/usr/lib/scons-2.1.0/SCons/Script/SConscript.py", line 551, in SConscriptreturn _SConscript(self.fs, *files,**subst_kw)
File "/usr/lib/scons-2.1.0/SCons/Script/SConscript.py", line 260, in _SConscri pt
exec _file_ in call_stack[-1].globals
File "/home/user/rosetta/rosetta++/SConscript.src.rosetta++", line 198, in
command % os.path.join("build", "src", build.platform, "rosetta++"))
NameError: name 'command' is not defined
scons: done reading SConscript files.
scons: Building targets ...
g++ -o build/src/release/cygwin/1.7/32/x86/gcc/numeric/constants.o -c -std=c++98 -pipe -ffor-scope -W -Wall -pedantic -fno-exceptions -malign-double -march=pent ium4 -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s - Wno-unused-variable -std=c99 -pipe -ffor-scope -W -Wall -pedantic -fno-exception s -malign-double -march=pentium4 -O3 -ffast-math -funroll-loops -finline-functio ns -finline-limit=20000 -s -Wno-unused-variable -DNDEBUG -Isrc -Iexternal/includ e -Isrc/platform/cygwin/1.7/32/x86/gcc -Isrc/platform/cygwin/1.7/32/x86 -Isrc/pl atform/cygwin/1.7/32 -Isrc/platform/cygwin/1.7 -Isrc/platform/cygwin -I/usr/loca l/include -I/usr/include src/numeric/constants.cc
/usr/lib/gcc/i686-pc-cygwin/4.5.3/cc1plus.exe: error while loading shared librar ies: cygcloog-0.dll: cannot open shared object file: No such file or directory
scons: *** [build/src/release/cygwin/1.7/32/x86/gcc/numeric/constants.o] Error 1
scons: building terminated because of errors.

Please advise ASAP

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Rosetta++ - Build/Install

how to compile Rosetta with MPI option?

albumns — Wed, 07 Mar 2012 20:11:35 +0000

Dear:
I would like to compile Rosetta with 'extras=mpi' option but failed. It always said the following:

sh: mpiCC: command not found
scons: *** [build/src/release/linux/2.6/64/x86/gcc/mpi/apps/public/AbinitioRelax.o] Error 127
mpiCC -o build/src/release/linux/2.6/64/x86/gcc/mpi/protocols/forge/remodel/RemodelWorkingSet.os -c -isystem external/boost_1_46_1/boost/ -isystem external/boost_1_46_1/boost/ -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -fPIC -DNDEBUG -DUSEMPI -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_46_1 -Iexternal/dbio -I/usr/local/include -I/usr/include src/protocols/forge/remodel/RemodelWorkingSet.cc
scons: *** [build/src/release/linux/2.6/64/x86/gcc/mpi/protocols/forge/remodel/RemodelLoopMover.os] Error 127
scons: *** [build/src/release/linux/2.6/64/x86/gcc/mpi/protocols/forge/remodel/RemodelConstraintGenerator.os] Error 127
scons: *** [build/src/release/linux/2.6/64/x86/gcc/mpi/protocols/forge/remodel/ResidueVicinityRCG.os] Error 127
scons: *** [build/src/release/linux/2.6/64/x86/gcc/mpi/protocols/forge/remodel/RemodelAccumulator.os] Error 127
scons: *** [build/src/release/linux/2.6/64/x86/gcc/mpi/protocols/forge/remodel/RemodelEnzdesCstModule.os] Error 127
scons: *** [build/src/release/linux/2.6/64/x86/gcc/mpi/protocols/forge/remodel/RemodelData.os] Error 127
sh: mpiCC: command not found
scons: *** [build/src/release/linux/2.6/64/x86/gcc/mpi/protocols/forge/remodel/RemodelWorkingSet.os] Error 127
scons: building terminated because of errors.

I also tried

ln -s site.settings.killdevil site.settings

but it doesn't work. the problem is the same.

THX

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Forums:

Rosetta 3 - Build/Install

Rosetta have graphical user interface

ajaniharesh — Tue, 21 Feb 2012 10:13:48 +0000

Hello Everyone

I am new in rosetta software. Rosetta software runing on command line software.

Is there available any graphical user interface version.

Thanks and Regards,

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Solved

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Rosetta++ - Build/Install