; When using this new tolopolgy, make sure you have included the required parameters ; (see http://swisssidechain.ch/MD/gromacs.html) [ 6CL ] ; 6-carboxylysine [ 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 HG2 HA 0.0900 8 HG1 HA 0.0900 9 CD CT2 -0.1800 10 HD1 HA 0.0900 11 HD2 HA 0.0900 12 CE CT1 0.2100 13 HE HA 0.1000 14 CZ CC 0.3400 15 NZ NH3 -0.3000 16 HZ1 HC 0.3300 17 HZ3 HC 0.3300 18 HZ2 HC 0.3300 19 OH1 OC -0.6700 20 OH2 OC -0.6700 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 OH1 CZ OH2 CZ CE CZ CD HD1 CE HE CD CE NZ CE HD2 CD CG CD CG HG2 CB HB2 NZ HZ1 CB CG HG1 CG HZ3 NZ HZ2 NZ HB1 CB [ impropers ] N -C CA HN C CA +N O CZ CE OH1 OH2 [ cmap ] -C N CA C +N