execution problem

[Flavio Seixas]

Hi,

I am having problems running g_mmpbsa ina CentOS 6.5 64bits:

[flavios@dhcppc0 ~]$ g_mmpbsa
g_mmpbsa: error while loading shared libraries: libgmx.so.8: cannot open shared object file: No such file or directory

I follow instalation instructions and no error appears.

I previously install gromacs 4.6.7 as suggested at "/opt/gromacs" directory and it is working fine, see below:

[flavios@dhcppc0 ~]$ mdrun
                         :-)  G  R  O  M  A  C  S  (-:

            Georgetown Riga Oslo Madrid Amsterdam Chisinau Stockholm

                            :-)  VERSION 4.6.7  (-:


Next, I install g_mmpbsa without errors, see below:

[root@dhcppc0 build]# cmake -DGMX_PATH=/opt/gromacs \
> -DAPBS_INSTALL=/opt/apbs \
> -DAPBS_SRC=/home/flavios/Downloads/apbs-1.3-source \
> -DFFTW_LIB=/home/flavios/Downloads/gromacs-4.6.7/build/src/contrib/fftw/fftwBuild-prefix/lib \
> -DCMAKE_INSTALL_PREFIX=/opt/g_mmpbsa \
> ..
-- The C compiler identification is GNU 4.4.7
-- The CXX compiler identification is GNU 4.4.7
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- The Fortran compiler identification is GNU
-- Check for working Fortran compiler: /usr/bin/gfortran
-- Check for working Fortran compiler: /usr/bin/gfortran  -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/bin/gfortran supports Fortran 90
-- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes
-- Configuring done
-- Generating done
-- Build files have been written to: /home/flavios/Downloads/g_mmpbsa/build
[root@dhcppc0 build]# make
Scanning dependencies of target energy2bfac
[ 10%] Building C object src/CMakeFiles/energy2bfac.dir/energy2bfac.c.o
Linking C executable energy2bfac
[ 10%] Built target energy2bfac
Scanning dependencies of target g_mmpbsa
[ 20%] Building C object src/CMakeFiles/g_mmpbsa.dir/main.c.o
[ 30%] Building C object src/CMakeFiles/g_mmpbsa.dir/energy_mm.c.o
[ 40%] Building C object src/CMakeFiles/g_mmpbsa.dir/InputPBSA.c.o
[ 50%] Building C object src/CMakeFiles/g_mmpbsa.dir/nsc.c.o
[ 60%] Building C object src/CMakeFiles/g_mmpbsa.dir/PbsaPrep.c.o
[ 70%] Building C object src/CMakeFiles/g_mmpbsa.dir/psize.c.o
[ 80%] Building C object src/CMakeFiles/g_mmpbsa.dir/radius.c.o
[ 90%] Building C object src/CMakeFiles/g_mmpbsa.dir/apbs13_main.c.o
[100%] Building C object src/CMakeFiles/g_mmpbsa.dir/apbs13_routines.c.o
Linking Fortran executable g_mmpbsa
[100%] Built target g_mmpbsa
[root@dhcppc0 build]# make install
[ 10%] Built target energy2bfac
[100%] Built target g_mmpbsa
Install the project...
-- Install configuration: ""
-- Installing: /opt/g_mmpbsa/bin/g_mmpbsa
-- Installing: /opt/g_mmpbsa/bin/energy2bfac
[root@dhcppc0 build]#



I set the variables at my .bashrc file:

[flavios@dhcppc0 ~]$ more .bashrc
# .bashrc

# Source global definitions
if [ -f /etc/bashrc ]; then
    . /etc/bashrc
fi

# User specific aliases and functions

export PATH=${PATH}:/opt/g_mmpbsa/bin
export PATH=${PATH}:/opt/gromacs/bin


and the error persists:

[flavios@dhcppc0 ~]$ g_mmpbsa
g_mmpbsa: error while loading shared libraries: libgmx.so.8: cannot open shared object file: No such file or directory


What am I doing worng?
Is there something I forgot to set?

I appreciate any help.

Regards,

Flavio

[g_mmpbsa Mailing List]

It seems that Gromacs has been installed with shared libraries. Setting path of Gromacs installed libraries in bash file will help to solve this problem. So you can add the following command in your bash file to make g_mmpbsa run:

export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:PATH OF LIBRARY FOLDER OF GROMACS

[Flavio Seixas]

Thank you once again.
The program is working very fine now.

Regards,

Flavio