! When using this topology, make sure you've included the required parameters ! (see http://swisssidechain.ch/MD/charmm.html) RESI APM 1.00 ! m-amidinophenyl-3-alanine GROUP ATOM N NH1 -0.4700 ATOM HN H 0.3100 ATOM CA CT1 0.0700 ATOM HA HB 0.0900 GROUP ATOM CB CT2 -0.1800 ATOM HB2 HA 0.0900 ATOM HB1 HA 0.0900 GROUP ATOM CG CA 0.0000 GROUP ATOM CD1 CA -0.1150 ATOM HD1 HP 0.1150 GROUP ATOM CD2 CA -0.1150 ATOM HD2 HP 0.1150 GROUP ATOM CZ CA -0.1150 ATOM HZ HP 0.1150 GROUP ATOM CE2 CA -0.1150 ATOM HE2 HP 0.1150 GROUP ATOM CE1 CA -0.0300 ATOM CH C 0.73 ATOM NJ1 NCN -0.75 ATOM HJ12 HNCN 0.4500 ATOM HJ11 HNCN 0.4500 ATOM NJ2 NCN -0.75 ATOM HJ21 HNCN 0.4500 ATOM HJ22 HNCN 0.4500 GROUP ATOM C C 0.5100 ATOM O O -0.5100 BOND CB CA N HN N CA C CA C +N CA HA DOUBLE O C BOND NJ1 HJ12 BOND NJ1 HJ11 BOND CH NJ1 BOND CD1 HD1 BOND NJ2 HJ21 BOND CB HB2 BOND NJ2 CH BOND CE1 CH BOND HJ22 NJ2 BOND CE1 CD1 BOND CG CD1 BOND CZ CE1 BOND HB1 CB BOND CG CB BOND CD2 CG BOND HZ CZ BOND CE2 CZ BOND CE2 CD2 BOND HD2 CD2 BOND HE2 CE2 IMPR N -C CA HN C CA +N O IMPR CH CE1 NJ1 NJ2 CMAP -C N CA C N CA C +N IC -C CA *N HN 1.3551 126.4900 180.0000 115.4200 0.9996 IC -C N CA C 1.3551 126.4900 180.0000 114.4400 1.5390 IC N CA C +N 1.4592 114.4400 180.0000 116.8400 1.3558 IC +N CA *C O 1.3558 116.8400 180.0000 122.5200 1.2297 IC CA C +N +CA 1.5390 116.8400 180.0000 126.7700 1.4613 IC N C *CA CB 1.4592 114.4400 123.2300 111.0900 1.5461 IC N C *CA HA 1.4592 114.4400 -120.4500 106.3900 1.0840 IC CG CD1 CE1 CZ 1.38 119.90 0.47 119.74 1.40 IC CG CD1 CE1 CH 1.38 119.90 -179.71 120.13 1.48 IC CG CD2 CE2 HE2 1.38 120.28 -179.95 119.89 1.08 IC CD1 CG CD2 CE2 1.38 120.09 0.21 120.28 1.38 IC CD1 CG CD2 HD2 1.38 120.09 -179.74 119.85 1.08 IC CD1 CG CB HB1 1.38 119.93 149.77 109.45 1.09 IC CD1 CG CB HB2 1.38 119.93 29.79 109.52 1.09 IC CD1 CE1 CZ HZ 1.39 119.74 179.78 120.06 1.08 IC CD1 CE1 CH NJ1 1.39 120.13 0.17 120.03 1.30 IC CD1 CE1 CH NJ2 1.39 120.13 -179.82 119.97 1.38 IC CD2 CG CD1 CE1 1.38 120.09 -0.44 119.90 1.39 IC CD2 CG CD1 HD1 1.38 120.09 179.95 120.06 1.08 IC CE1 CH NJ1 HJ12 1.48 120.03 179.99 120.03 0.97 IC CE1 CH NJ1 HJ11 1.48 120.03 0.06 119.97 1.01 IC CE1 CH NJ2 HJ21 1.48 119.97 -179.99 119.92 0.97 IC CE1 CH NJ2 HJ22 1.48 119.97 -0.02 120.00 0.97 IC CD1 CB *CG CD2 0.00 0.00 180.00 0.00 0.00 IC CE1 CG *CD1 HD1 0.00 0.00 180.00 0.00 0.00 IC CE2 CG *CD2 HD2 0.00 0.00 180.00 0.00 0.00 IC CH CD1 *CE1 CZ 0.00 0.00 180.00 0.00 0.00 IC CA CG *CB HB2 0.00 0.00 120.00 0.00 0.00 IC HB2 CG *CB HB1 0.00 0.00 -120.00 0.00 0.00 IC C CB *CA N 0.00 0.00 120.00 0.00 0.00 IC C CB *CA HA 0.00 0.00 -120.00 0.00 0.00 IC NJ1 CE1 *CH NJ2 0.00 0.00 180.00 0.00 0.00 IC CZ CD2 *CE2 HE2 0.00 0.00 180.00 0.00 0.00 IC CE2 CE1 *CZ HZ 0.00 0.00 180.00 0.00 0.00 IC HJ12 CH *NJ1 HJ11 0.00 0.00 180.00 0.00 0.00 IC HJ21 CH *NJ2 HJ22 0.00 0.00 180.00 0.00 0.00