; When using this new tolopolgy, make sure you have included the required parameters ; (see http://swisssidechain.ch/MD/gromacs.html) [ DTH9 ] ; 3-(3-benzothienyl)-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 CY -0.0300 7 CD2 CPT -0.0200 8 CD1 CA -0.0900 9 HD1 HP 0.1500 10 CE3 CA -0.1150 11 HE3 HP 0.1150 12 CE2 CPT 0.0700 13 SE1 STHI -0.0800 14 CZ3 CA -0.1150 15 HZ3 HP 0.1150 16 CZ2 CA -0.1150 17 HZ2 HP 0.1150 18 CH2 CA -0.1150 19 HH2 HP 0.1150 20 C C 0.5100 21 O O -0.5100 22 [ bonds ] N HN N CA C CA C +N CA HA CB CA O C CZ3 HZ3 CH2 HH2 CH2 CZ3 CE3 CZ3 CZ2 CH2 CE3 HE3 CD2 CE3 HZ2 CZ2 CE2 CZ2 CE2 CD2 CG CD2 SE1 CE2 CB HB2 CB CG CD1 CG HB1 CB CD1 SE1 HD1 CD1 [ impropers ] N -C CA HN C CA +N O [ cmap ] -C N CA C +N