I am attaching a drive link here in which there is a screenshot of DALA-6 ramachandran plot and there you can see some dihedral angle come in second quadrant and some in 3rd which is not allowed region for D aminoacid.
and in gromacs files that i have attached there are all files including initial structure, mdp files that i have generated by charmm gui.
link- check - Google Drive
please have a look and do comment if something seems wrong