; When using this new tolopolgy, make sure you have included the required parameters ; (see http://swisssidechain.ch/MD/gromacs.html) [ PYR2 ] ; 3-(2-Pyridyl)-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 0.1600 9 HE1 HP 0.1500 10 CD2 CA -0.1150 11 HD2 HP 0.1150 12 CE2 CA -0.1150 13 HE2 HP 0.1150 14 CZ CA -0.1150 15 HZ HP 0.1150 16 C C 0.5100 17 O O -0.5100 18 [ bonds ] N HN N CA C CA C +N CA HA CB CA O C CG CB HB1 CB HB2 CB CE2 CD2 CG CD2 HD2 CD2 CZ CE1 HE1 CE1 ND1 CE1 CZ CE2 HE2 CE2 ND1 CG HZ CZ [ impropers ] N -C CA HN C CA +N O [ cmap ] -C N CA C +N