; When using this new tolopolgy, make sure you have included the required parameters ; (see http://swisssidechain.ch/MD/gromacs.html) [ IGL ] ; 3-methyl-l-alloisoleucine [ atoms ] N NH1 -0.4700 0 HN H 0.3100 1 CA CT1 0.0700 2 HA HB 0.0900 3 CB CT1 -0.0900 4 HB HA 0.0900 5 CG1 CT2 -0.1800 6 HG11 HA 0.0900 7 HG12 HA 0.0900 8 CG2 CT2 -0.1800 9 HG21 HA 0.0900 10 HG22 HA 0.0900 11 CD1 CA 0.0000 12 CD2 CA 0.0000 13 CE1 CA -0.1150 14 HE1 HP 0.1150 15 CE2 CA -0.1150 16 HE2 HP 0.1150 17 CH1 CA -0.1150 18 HH1 HP 0.1150 19 CH2 CA -0.1150 20 HH2 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 CG1 CB CG2 CB HB CB CE1 CD1 CG1 CD1 CD2 CD1 CG2 CD2 CE2 CD2 CH1 CE1 HE1 CE1 CH2 CE2 HE2 CE2 HG11 CG1 HG12 CG1 HG21 CG2 HG22 CG2 CH2 CH1 HH1 CH1 HH2 CH2 [ impropers ] N -C CA HN C CA +N O [ cmap ] -C N CA C +N