/usr/share/man/man1/pdb2gmx_d.1.gz is in gromacs-data 4.6.5-1build1.
This file is owned by root:root, with mode 0o777.
It is a symlink to /usr/share/man/man1/pdb2gmx.1.gz
/usr/share/man/man1/pdb2gmx.1.gz