Rosetta fragment tools installation error

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Dear Friends,

I am trying to install rosetta on my local system, but facing issues because of CSBLAST. The latest rosetta bunble I downloaded from rosetta website is : rosetta_src_2019.31.60840_bundle.

After that, since I want to perform "ab initio structure prediction", I am following this tutorial:

https://www.rosettacommons.org/demos/latest/tutorials/denovo_structure_prediction/Denovo_structure_prediction

In this tutorial, there is a "fragment picking" tutorial:: https://www.rosettacommons.org/demos/latest/public/fragment_picking/README

I am following this tutorila to make fragments for de novo structure prediction; however, I am stuck at this step:

Put this vall in the flags:

$ <path-to-Rosetta>/main/database/sampling/filtered.vall.dat.2006-05-05.gz

Update the flags with your correct database location
Run the picker like this:

To accomplish this step, I went to "tools/fragment_tools/" folder of the bundle and ran "install-dependencies.pl", but it gave me error for CSBLAST package saying:

/usr/bin/g++ -O3 -DNDEBUG -fopenmp -DOPENMP -Wall -Wno-deprecated -m64 -DCOMPILER_OPTIONS="\"-O3 -DNDEBUG -fopenmp -DOPENMP -Wall -Wno-deprecated -m64\"" -fno-strict-aliasing -DVERSION="\"2.2.3\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -I$HOME/include -c -o ../build/application.o application.cc

In file included from csblast_app.cc:21:0:

alignment-inl.h: In function ‘Vector<double> cs::PositionSpecificWeightsAndDiversity(const cs::Alignment<Abc>&, Matrix<double>&)’:

alignment-inl.h:842:16: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else]

if (ncoli < kMinCols) // number of columns in subalignment insufficient?

In file included from pseudocounts-inl.h:22:0,

from context_library.h:26,

from csblast_app.cc:25:

pseudocounts.h: At global scope:

pseudocounts.h:172:25: error: ‘constexpr’ needed for in-class initialization of static data member ‘const double cs::Pseudocounts<Abc>::kNormalize’ of non-integral type [-fpermissive]

static const double kNormalize = 1e-5; // Normalization threshold.

^~~~~~~~~~

pseudocounts.h:173:25: error: ‘constexpr’ needed for in-class initialization of static data member ‘const double cs::Pseudocounts<Abc>::kTargetNeffParamMin’ of non-integral type [-fpermissive]

static const double kTargetNeffParamMin = 0.0; // Minimal paramater value for adjusting to the target Neff.

^~~~~~~~~~~~~~~~~~~

pseudocounts.h:174:25: error: ‘constexpr’ needed for in-class initialization of static data member ‘const double cs::Pseudocounts<Abc>::kTargetNeffParamMax’ of non-integral type [-fpermissive]

static const double kTargetNeffParamMax = 1.0; // Maximal parameter value for adjusting to the target Neff.

^~~~~~~~~~~~~~~~~~~

pseudocounts.h:175:25: error: ‘constexpr’ needed for in-class initialization of static data member ‘const double cs::Pseudocounts<Abc>::kTargetNeffParamInit’ of non-integral type [-fpermissive]

static const double kTargetNeffParamInit = 0.5; // Initial parameter value for adjusting to the target Neff.

^~~~~~~~~~~~~~~~~~~~

pseudocounts.h:176:25: error: ‘constexpr’ needed for in-class initialization of static data member ‘const double cs::Pseudocounts<Abc>::kTargetNeffEps’ of non-integral type [-fpermissive]

static const double kTargetNeffEps = 0.01; // Convergence threshold for adjusting to the target Neff.

^~~~~~~~~~~~~~

pseudocounts.h: In instantiation of ‘class cs::Pseudocounts<cs::AA>’:

csblast_app.cc:327:38: required from here

pseudocounts.h:172:25: error: ‘constexpr’ needed for in-class initialization of static data member ‘const double cs::Pseudocounts<cs::AA>::kNormalize’ of non-integral type [-fpermissive]

static const double kNormalize = 1e-5; // Normalization threshold.

^~~~~~~~~~

pseudocounts.h:173:25: error: ‘constexpr’ needed for in-class initialization of static data member ‘const double cs::Pseudocounts<cs::AA>::kTargetNeffParamMin’ of non-integral type [-fpermissive]

static const double kTargetNeffParamMin = 0.0; // Minimal paramater value for adjusting to the target Neff.

^~~~~~~~~~~~~~~~~~~

pseudocounts.h:174:25: error: ‘constexpr’ needed for in-class initialization of static data member ‘const double cs::Pseudocounts<cs::AA>::kTargetNeffParamMax’ of non-integral type [-fpermissive]

static const double kTargetNeffParamMax = 1.0; // Maximal parameter value for adjusting to the target Neff.

^~~~~~~~~~~~~~~~~~~

pseudocounts.h:175:25: error: ‘constexpr’ needed for in-class initialization of static data member ‘const double cs::Pseudocounts<cs::AA>::kTargetNeffParamInit’ of non-integral type [-fpermissive]

static const double kTargetNeffParamInit = 0.5; // Initial parameter value for adjusting to the target Neff.

^~~~~~~~~~~~~~~~~~~~

pseudocounts.h:176:25: error: ‘constexpr’ needed for in-class initialization of static data member ‘const double cs::Pseudocounts<cs::AA>::kTargetNeffEps’ of non-integral type [-fpermissive]

static const double kTargetNeffEps = 0.01; // Convergence threshold for adjusting to the target Neff.

^~~~~~~~~~~~~~

Makefile:129: recipe for target '../build/csblast_app.o' failed

make: *** [../build/csblast_app.o] Error 1

Hence, "install_dependencies.pl" did not work, so I cannot run "make_fragments.pl", and thus, no vall files. could you please let me know how can I resolve this issue? I need to perform ab initio structure prediction for a 382 residue long phage tail protein. Your suggestions are very welcome.

Regards

Category:

Structure prediction

Post Situation:

Unsolved

Thu, 2019-08-29 02:17

Danielsebas

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Hello,

I believe your gcc/g++ version is too new, I don't see the error with gcc5.4/g++5.4

as an alternative you could have the robetta server build your fragments for you here:

http://robetta.bakerlab.org/fragmentsubmit.jsp

Thu, 2019-08-29 08:05

danpf

(Reply to #3)

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Yes that was the reason. I degraded gcc to version 5.5 and it worked.

Sun, 2019-09-01 02:38

Danielsebas

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Rosetta fragment tools installation error