; When using this new tolopolgy, make sure you have included the required parameters ; (see http://swisssidechain.ch/MD/gromacs.html) [ NAL ] ; 2-Naphtalene [ atoms ] N NH1 -0.4700 0 HN H 0.3100 1 CA CT1 0.0700 2 HA HB 0.0900 3 CB CT2 -0.1800 4 HB1 HA 0.0900 5 HB2 HA 0.0900 6 CG CA 0.0000 7 CD2 CA -0.1150 8 HD2 HP 0.1150 9 CD1 CA -0.1150 10 HD1 HP 0.1150 11 CE2 CA 0.0000 12 CE1 CA -0.1150 13 HE1 HP 0.1150 14 CZ CA 0.0000 15 CH2 CA -0.1150 16 HH2 HP 0.1150 17 CH1 CA -0.1150 18 HH1 HP 0.1150 19 CJ2 CA -0.1150 20 HJ2 HP 0.1150 21 CJ1 CA -0.1150 22 HJ1 HP 0.1150 23 C C 0.5100 24 O O -0.5100 25 [ bonds ] N HN N CA C CA C +N CA HA CB CA O C CG CB CG CD2 CD1 CG CD2 CE2 CZ CE2 CH2 CE2 CE1 CD1 CZ CE1 CH1 CZ CJ1 CH1 CJ2 CJ1 CH2 CJ2 HB1 CB HB2 CB HD2 CD2 HD1 CD1 HE1 CE1 HH1 CH1 HJ1 CJ1 HJ2 CJ2 HH2 CH2 [ impropers ] N -C CA HN C CA +N O [ cmap ] -C N CA C +N