Compiling Aria2, CNS, procheck and aqua for NMR structure calculation

A quick guide to compiling ARIA 2.2, CNS 1.21, AQUA 3.2 and PROCHECK, under Ubuntu Karmic 9.10 (32-bit)

If you use Gentoo linux, you can find aria under sci-chemistry (masked by ~x86). Procheck is in the science overlay (see the layman and overlays documentation). Aqua has to be installed manually at the time of writing this post.

In Ubuntu, the following packages are needed:

  • numpy
  • scipy
  • python-scientific
  • tcl 8.5
  • tk 8.5
  • tix
  • matplotlib
  • cns (to be compiled manually, see below)
  • the intel fortran compiler (to compile cns, gfortran does not seem to work)
  • tcsh
  • openjdk6 (needed for intel fortran compiler)
  • libstdc++5 (for cns)
  • flex (for cns)

Some files need to be copied from ARIA to CNS before it is compiled, this can be found in the ARIA instructions. Both CNS and ARIA can be compiled according to the instructions, but during the compilation of CNS with gfortran 4.3 I got a Segmentation fault. Using the Intel fortran compiler (ifort, free for academic use), there were no problems. For the installation of the Intel compiler, I needed to have openjdk6, which I installed using the Synaptic "default_jre" package.

CNS required libstdc++5 (download the old .deb) and flex ("lex" command not found) to compile correctly.

Procheck and aqua can be installed according to the instructions. I used ifort to compile procheck, and g++ for aqua.

And here are the lines to include in .tcshrc (of course substituting the directories for the ones that are used on your system):

# for cns:
source /home/louic/software/cns_solve_1.21/cns_solve_env
# for aria:
setenv ARIA2 '/home/louic/software/aria2.2'
alias aria2 '/usr/bin/python -O $ARIA2/'
# for procheck and aqua:
setenv prodir '/home/louic/software/procheck'
setenv aquaroot '/home/louic/software/aqua3.2'
source $aquaroot/aqsetup

There seemed to be some problems on a 64-bit system, which is why I switched back to using 32-bit for now. I did not fully investigate this issue and do not know what the exact problem was.

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