; When using this new tolopolgy, make sure you have included the required parameters ; (see http://swisssidechain.ch/MD/gromacs.html) [ DALN ] ; 1-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 CD1 CA 0.0000 8 CD2 CA -0.1150 9 HD2 HP 0.1150 10 CE1 CA 0.0000 11 CH1 CA -0.1150 12 HH1 HP 0.1150 13 CE2 CA -0.1150 14 HE2 HP 0.1150 15 CH2 CA -0.1150 16 HH2 HP 0.1150 17 CZ CA -0.1150 18 HZ HP 0.1150 19 CJ1 CA -0.1150 20 HJ1 HP 0.1150 21 CJ2 CA -0.1150 22 HJ2 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 CE1 CD1 CH1 CD1 CG CD1 CE2 CD2 CG CD2 CH2 CE1 CZ CE1 CZ CE2 CJ1 CH1 CJ2 CH2 CJ2 CJ1 CB HB1 CB HB2 CD2 HD2 CE2 HE2 CZ HZ CJ1 HJ1 CJ2 HJ2 CH1 HH1 CH2 HH2 [ impropers ] N -C CA HN C CA +N O [ cmap ] -C N CA C +N