; When using this new tolopolgy, make sure you have included the required parameters ; (see http://swisssidechain.ch/MD/gromacs.html) [ THA3 ] ; 3-(3-thienyl)-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 HB1 HA 0.0900 5 HB2 HA 0.0900 6 CG C5B 0.0000 7 CD1 C5A -0.1100 8 HD1 HP 0.1500 9 CD2 C5B -0.1500 10 HD2 HP 0.1500 11 SE1 STHI -0.0800 12 CE2 C5A -0.1100 13 HE2 HP 0.1500 14 C C 0.5100 15 O O -0.5100 16 [ bonds ] N HN N CA C CA C +N CA HA CB CA O C CG CB HB1 CB HB2 CB CG CD1 SE1 CD1 CE2 CD2 CG CD2 SE1 CE2 CD2 HD2 CE2 HE2 CD1 HD1 [ impropers ] N -C CA HN C CA +N O CD1 CG SE1 HD1 CD2 CG CE2 HD2 CE2 CD2 SE1 HE2 [ cmap ] -C N CA C +N