; When using this new tolopolgy, make sure you have included the required parameters ; (see http://swisssidechain.ch/MD/gromacs.html) [ DAPM ] ; m-amidinophenyl-3-alanine [ atoms ] N NH1 -0.4700 0 HN H 0.3100 1 CA CT1 0.0700 2 HA HB 0.0900 3 CB CT2 -0.1800 4 HB2 HA 0.0900 5 HB1 HA 0.0900 6 CG CA 0.0000 7 CD1 CA -0.1150 8 HD1 HP 0.1150 9 CD2 CA -0.1150 10 HD2 HP 0.1150 11 CZ CA -0.1150 12 HZ HP 0.1150 13 CE2 CA -0.1150 14 HE2 HP 0.1150 15 CE1 CA -0.0300 16 CH C 0.7300 17 NJ1 NCN -0.7500 18 HJ12 HNCN 0.4500 19 HJ11 HNCN 0.4500 20 NJ2 NCN -0.7500 21 HJ21 HNCN 0.4500 22 HJ22 HNCN 0.4500 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 NJ1 HJ12 NJ1 HJ11 CH NJ1 CD1 HD1 NJ2 HJ21 CB HB2 NJ2 CH CE1 CH HJ22 NJ2 CE1 CD1 CG CD1 CZ CE1 HB1 CB CG CB CD2 CG HZ CZ CE2 CZ CE2 CD2 HD2 CD2 HE2 CE2 [ impropers ] N -C CA HN C CA +N O CH CE1 NJ1 NJ2 [ cmap ] -C N CA C +N