; When using this new tolopolgy, make sure you have included the required parameters ; (see http://swisssidechain.ch/MD/gromacs.html) [ DALC ] ; 3-cyclohexyl-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 CT1 -0.0900 7 HG HA 0.0900 8 CD1 CT2 -0.1800 9 HD11 HA 0.0900 10 HD12 HA 0.0900 11 CD2 CT2 -0.1800 12 HD21 HA 0.0900 13 HD22 HA 0.0900 14 CE1 CT2 -0.1800 15 HE11 HA 0.0900 16 HE12 HA 0.0900 17 CE2 CT2 -0.1800 18 HE21 HA 0.0900 19 HE22 HA 0.0900 20 CZ CT2 -0.1800 21 HZ1 HA 0.0900 22 HZ2 HA 0.0900 23 C C 0.5100 24 O O -0.5100 25 [ bonds ] N HN N CA C CA C +N CA HA CB CA O C CG CB HB1 CB HB2 CB CE1 CD1 CG CD1 CE2 CD2 CG CD2 CZ CE1 CZ CE2 CG HG CD1 HD11 CD1 HD12 CE1 HE11 CE1 HE12 CZ HZ1 CZ HZ2 CE2 HE21 CE2 HE22 CD2 HD21 CD2 HD22 [ impropers ] N -C CA HN C CA +N O [ cmap ] -C N CA C +N