; When using this new tolopolgy, make sure you have included the required parameters ; (see http://swisssidechain.ch/MD/gromacs.html) [ PYR4 ] ; 3-(4-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 0.0000 7 CD1 CA -0.1150 8 HD1 HP 0.1150 9 CD2 CA -0.1150 10 HD2 HP 0.1150 11 CE1 CA 0.1600 12 HE1 HP 0.1500 13 CE2 CA 0.1600 14 HE2 HP 0.1500 15 NZ NPYD -0.6200 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 CE1 CD1 CG CD1 CE2 CD2 CG CD2 NZ CE1 NZ CE2 CB HB1 CB HB2 CD1 HD1 CD2 HD2 CE1 HE1 CE2 HE2 [ impropers ] N -C CA HN C CA +N O [ cmap ] -C N CA C +N