; When using this new tolopolgy, make sure you have included the required parameters ; (see http://swisssidechain.ch/MD/gromacs.html) [ C2N ] ; 3-chloro-d-alanine [ atoms ] N NH1 -0.4700 0 HN H 0.3100 1 CA CT1 0.0700 2 HA HB 0.0900 3 CB CT2 0.1100 4 HB1 HA 0.0900 5 HB2 HA 0.0900 6 CL CLAL -0.2900 7 C C 0.5100 8 O O -0.5100 9 [ bonds ] N HN N CA C CA C +N CA HA CB CA O C CB CL HB1 CB HB2 CB [ impropers ] N -C CA HN C CA +N O [ cmap ] -C N CA C +N