; When using this new tolopolgy, make sure you have included the required parameters ; (see http://swisssidechain.ch/MD/gromacs.html) [ D2NP ] ; l-2-amino-6-methylene-pimelic acid [ 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 CT2 -0.1800 7 HG1 HA 0.0900 8 HG2 HA 0.0900 9 CD CT2 -0.1800 10 HD2 HA 0.0900 11 HD1 HA 0.0900 12 CE C=C -0.3800 13 CZ1 CC 0.9000 14 CZ2 CE2 -0.3000 15 HZ22 HE2 0.1500 16 HZ21 HE2 0.1500 17 OJ1 OC -0.7600 18 OJ2 OC -0.7600 19 C C 0.5100 20 O O -0.5100 21 [ bonds ] N HN N CA C CA C +N CA HA CB CA O C OJ1 CZ1 OJ2 CZ1 CB HB2 CB HB1 CD HD2 CG CB CD HD1 CG CD CE CD HG1 CG HG2 CG CZ1 CE CZ2 CE CZ2 HZ22 HZ21 CZ2 [ impropers ] N -C CA HN C CA +N O CE CD CZ1 CZ2 CZ1 CE OJ1 OJ2 CZ2 CE HZ21 HZ22 [ cmap ] -C N CA C +N