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orbeckst / gridcount

DEPRECATED and UNSUPPORTED. gridcount is an analysis tool for Gromacs that creates 3D (number) densities from molecular dynamics trajectories. Typically, this is used to look at the density of water or ions near proteins or in channels. It provides tools to generate the 3D map in portable formats, 2D cylindrical averages and 1D linear averages ("density profiles").
http://sbcb.bioch.ox.ac.uk/oliver/software/#gridcount
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error while loading shared libraries: libmd.so.6 #5

Closed orbeckst closed 9 years ago

orbeckst commented 9 years ago

Karim Mahnam (via email)

I want to calculate 3D density of ions around my protein via gridcount. I have installed and configured Gromacs 4.5.3 with "--enable-shared" option. I compiled and installed gridcount-gridcount-gmx-4.5.1.4 without any error and it make g_ri3Dc and a_ri3Dc bineries in /usr/local/gromacs/bin , but when I want to run g_ri3Dc or a_ri3Dc, it says "command not found" or when I run it in bin directory of gromacs it says "error while loading shared libraries: libmd.so.6: cannot open shared object file: No such file or directory"

Would you please tell me how can i solve this problem and how can obtain 3D density of ions around my protein.

orbeckst commented 9 years ago

It sound if your dynamic libraries are not found. Try setting the environment variable LD_LIBRARY_PATH to the location of your Gromacs libs (see http://tldp.org/HOWTO/Program-Library-HOWTO/shared-libraries.html )

Maybe it's sufficient to source GMXRC.

By the way, you can set PATH if the binaries are not found automatically.