; When using this new tolopolgy, make sure you have included the required parameters ; (see http://swisssidechain.ch/MD/gromacs.html) [ DQX3 ] ; 3-(2-quinoxalyl)-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 CA 0.3100 7 ND1 NPYD -0.6200 8 CE1 CA 0.3100 9 CD2 CA 0.1600 10 HD2 HP 0.1500 11 NE2 NPYD -0.6200 12 CZ CA 0.3100 13 CH1 CA -0.1150 14 HH1 HP 0.1150 15 CH2 CA -0.1150 16 HH2 HP 0.1150 17 CJ1 CA -0.1150 18 HJ1 HP 0.1150 19 CJ2 CA -0.1150 20 HJ2 HP 0.1150 21 C C 0.5100 22 O O -0.5100 23 [ bonds ] N HN N CA C CA C +N CA HA CB CA O C CG CB CG CD2 ND1 CG NE2 CZ CD2 NE2 CE1 ND1 CJ1 CH1 CJ2 CJ1 CH2 CJ2 CE1 CZ CH2 CZ CH1 CE1 CB HB1 CB HB2 CD2 HD2 CH1 HH1 CJ1 HJ1 CJ2 HJ2 CH2 HH2 [ impropers ] N -C CA HN C CA +N O [ cmap ] -C N CA C +N