There is a bug in the do_dssp command in GROMACS 4.5.5 that prevents the analysis of secondary structure using DSSP . Attempting to run do_dssp will result in a segmentation fault. The bug has been patched since 4.5.5, but this version has not been released (see this post on the GROMACS mailing list). To get the patched version, follow the instructions from this post.
git clone git://git.gromacs.org/gromacs.git git checkout --track -b release-4-5-patches origin/release-4-5-patches
On our Red Hat Enterprise Linux cluster, I built the patched version of GROMACS and linked it against FFTW3. Here is the FFTW3 configure command that I used:
./configure --prefix=/apps/fftw3_shared_intel_openmpi --enable-float --enable-mpi --enable-openmp --enable-threads --enable-shared
I used the following command to configure GROMACS:
CPPFLAGS="-I/apps/fftw3_shared_intel_openmpi/include" LDFLAGS="-L/apps/fftw3_shared_intel_openmpi/lib" ./configure --enable-mpi --prefix=/apps/gromacs-4.5.5-patched-intel-openmpi-fftw3/
Note that we have adopted a convention of installing non-system software in the /apps directory instead of one of the conventional Linux directories. This allows us to keep our base RHEL system clean and stable.
There are two versions of DSSP. GROMACS will only work with the old version of DSSP! Download the old version of DSSP from this site. I downloaded the Linux binary executable, and it worked fine on our system. You’ll have to change the file permissions to make it executable after you download it. Make sure you set the environment variable DSSP to point to the DSSP binary, as described in the do_dssp manual page.