; ; Encad residue topology file. ; Note that this is only a subset of all molecules described ; in Encad. If you need to use a new one, it might help to ; study the parameter files of Encad. ; [ bondedtypes ] ; bonds angles dihedrals impropers all_dihedrals nrexcl keep_dihedrals_on_impropers 1 1 1 1 0 3 1 [ ACE ] [ atoms ] CH3 C3 -0.357 1 HH31 H 0.119 1 HH32 H 0.119 1 HH33 H 0.119 1 C Aprime 0.380 2 O O -0.380 2 [ bonds ] CH3 HH31 CH3 HH32 CH3 HH33 CH3 C C O [ dihedrals ] HH33 CH3 C +N CH3 C +N +CA [ impropers ] C HH33 CH3 HH31 improper_X_X_C_X C HH33 CH3 HH32 improper_X_X_C_X CH3 +N C O improper_X_X_A_X [ ALA ] [ atoms ] N N1 -0.333 0 H HN 0.333 0 CA C1 -0.119 1 HA H 0.119 1 CB C3 -0.357 2 HB1 H 0.119 2 HB2 H 0.119 2 HB3 H 0.119 2 C Aprime 0.380 3 O O -0.380 3 [ bonds ] N H N CA CA HA CA CB CA C CB HB1 CB HB2 CB HB3 C O -C N [ dihedrals ] -CA -C N CA -C N CA C N CA CB HB3 N CA C +N [ impropers ] -C CA N H improper_X_X_N_X N C CA HA improper_X_X_C_X N C CA CB improper_N_A_C1_C CA HB3 CB HB1 improper_X_X_C_X CA HB3 CB HB2 improper_X_X_C_X CA +N C O improper_X_X_A_X [ ARG ] [ atoms ] N N1 -0.333 0 H HN 0.333 0 CA C1 -0.119 1 HA H 0.119 1 CB C2 -0.238 2 HB1 H 0.119 2 HB2 H 0.119 2 CG C2 -0.238 3 HG1 H 0.119 3 HG2 H 0.119 3 CD C2 -0.238 4 HD1 H 0.119 4 HD2 H 0.119 4 NE M1 -0.333 5 HE HN 0.533 5 CZ A6 0.000 6 NH1 M2 -0.666 7 HH11 HN 0.533 7 HH12 HN 0.533 7 NH2 M2 -0.666 8 HH21 HN 0.533 8 HH22 HN 0.533 8 C Aprime 0.380 9 O O -0.380 9 [ bonds ] N H N CA CA HA CA CB CA C CB HB1 CB HB2 CB CG CG HG1 CG HG2 CG CD CD HD1 CD HD2 CD NE NE HE NE CZ CZ NH1 CZ NH2 NH1 HH11 NH1 HH12 NH2 HH21 NH2 HH22 C O -C N [ dihedrals ] -CA -C N CA -C N CA C N CA CB CG N CA C +N CA CB CG CD CB CG CD NE CG CD NE CZ CD NE CZ NH2 NE CZ NH1 HH12 NE CZ NH2 HH22 [ impropers ] -C CA N H improper_X_X_N_X N C CA HA improper_X_X_C_X N C CA CB improper_N_A_C1_C CA +N C O improper_X_X_A_X CA CG CB HB1 improper_X_X_C_X CA CG CB HB2 improper_X_X_C_X CB CD CG HG1 improper_X_X_C_X CB CD CG HG2 improper_X_X_C_X CG NE CD HD1 improper_X_X_C_X CG NE CD HD2 improper_X_X_C_X CD CZ NE HE improper_X_X_M_X NE NH2 CZ NH1 improper_X_X_A_X CZ HH12 NH1 HH11 improper_X_X_M_X CZ HH22 NH2 HH21 improper_X_X_M_X [ ARGN ] [ atoms ] N N1 -0.333 0 H HN 0.333 0 CA C1 -0.119 1 HA H 0.119 1 CB C2 -0.238 2 HB1 H 0.119 2 HB2 H 0.119 2 CG C2 -0.238 3 HG1 H 0.119 3 HG2 H 0.119 3 CD C2 -0.238 4 HD1 H 0.119 4 HD2 H 0.119 4 NE M1 -0.333 5 HE HN 0.333 5 CZ A6 0.000 6 NH1 M1 -0.333 7 HH1 HN 0.333 7 NH2 M2 -0.666 8 HH21 HN 0.333 8 HH22 HN 0.333 8 C Aprime 0.380 9 O O -0.380 9 [ bonds ] N H N CA CA HA CA CB CA C CB HB1 CB HB2 CB CG CG HG1 CG HG2 CG CD CD HD1 CD HD2 CD NE NE HE NE CZ CZ NH1 CZ NH2 NH1 HH1 NH2 HH21 NH2 HH22 C O -C N [ dihedrals ] -CA -C N CA -C N CA C N CA CB CG N CA C +N CA CB CG CD CB CG CD NE CG CD NE CZ CD NE CZ NH2 NE CZ NH1 HH1 NE CZ NH2 HH22 [ impropers ] -C CA N H improper_X_X_N_X N C CA HA improper_X_X_C_X N C CA CB improper_N_A_C1_C CA +N C O improper_X_X_A_X CA CG CB HB1 improper_X_X_C_X CA CG CB HB2 improper_X_X_C_X CB CD CG HG1 improper_X_X_C_X CB CD CG HG2 improper_X_X_C_X CG NE CD HD1 improper_X_X_C_X CG NE CD HD2 improper_X_X_C_X CD CZ NE HE improper_X_X_M_X NE NH1 CZ NH2 improper_X_X_A_X CZ HH21 NH2 HH22 improper_X_X_M_X [ ASN ] [ atoms ] N N1 -0.333 0 H HN 0.333 0 CA C1 -0.119 1 HA H 0.119 1 CB C2 -0.238 2 HB1 H 0.119 2 HB2 H 0.119 2 CG Aprime 0.380 3 OD1 O -0.380 3 ND2 N2 -0.666 4 HD21 HN 0.333 4 HD22 HN 0.333 4 C Aprime 0.380 5 O O -0.380 5 [ bonds ] N H N CA CA HA CA CB CA C CB HB1 CB HB2 CB CG CG OD1 CG ND2 ND2 HD21 ND2 HD22 C O -C N [ dihedrals ] -CA -C N CA -C N CA C N CA CB CG N CA C +N CA CB CG ND2 CB CG ND2 HD22 [ impropers ] -C CA N H improper_X_X_N_X N C CA HA improper_X_X_C_X N C CA CB improper_N_A_C1_C CA +N C O improper_X_X_A_X CA CG CB HB1 improper_X_X_C_X CA CG CB HB2 improper_X_X_C_X CB ND2 CG OD1 improper_X_X_A_X CG HD22 ND2 HD21 improper_X_X_N_X [ ASP ] [ atoms ] N N1 -0.333 0 H HN 0.333 0 CA C1 -0.119 1 HA H 0.119 1 CB C2 -0.238 2 HB1 H 0.119 2 HB2 H 0.119 2 CG Abis 0.840 3 OD1 Obis -0.920 3 OD2 Obis -0.920 3 C Aprime 0.380 4 O O -0.380 4 [ bonds ] N H N CA CA HA CA CB CA C CB HB1 CB HB2 CB CG CG OD1 CG OD2 C O -C N [ dihedrals ] -CA -C N CA -C N CA C N CA CB CG N CA C +N CA CB CG OD2 [ impropers ] -C CA N H improper_X_X_N_X N C CA HA improper_X_X_C_X N C CA CB improper_N_A_C1_C CA +N C O improper_X_X_A_X CA CG CB HB1 improper_X_X_C_X CA CG CB HB2 improper_X_X_C_X CB OD2 CG OD1 improper_X_X_A_X [ ASPH ] [ atoms ] N N1 -0.333 0 H HN 0.333 0 CA C1 -0.119 1 HA H 0.119 1 CB C2 -0.238 2 HB1 H 0.119 2 HB2 H 0.119 2 CG Aprime 0.380 3 OD1 O -0.380 3 OD2 OH -0.433 4 HD2 HO 0.433 4 C Aprime 0.380 5 O O -0.380 5 [ bonds ] N H N CA CA HA CA CB CA C CB HB1 CB HB2 CB CG CG OD1 CG OD2 OD2 HD2 C O -C N [ dihedrals ] -CA -C N CA -C N CA C N CA CB CG N CA C +N CA CB CG OD2 CB CG OD2 HD2 [ impropers ] -C CA N H improper_X_X_N_X N C CA HA improper_X_X_C_X N C CA CB improper_N_A_C1_C CA +N C O improper_X_X_A_X CA CG CB HB1 improper_X_X_C_X CA CG CB HB2 improper_X_X_C_X OD2 CB CG OD1 improper_X_X_A_X [ CYS2 ] ; aka CYX [ atoms ] N N1 -0.333 0 H HN 0.333 0 CA C1 -0.119 1 HA H 0.119 1 CB C2 -0.238 2 HB1 H 0.119 2 HB2 H 0.119 2 SG S 0.000 3 C Aprime 0.380 4 O O -0.380 4 [ bonds ] N H N CA CA HA CA CB CA C CB HB1 CB HB2 CB SG C O -C N [ dihedrals ] -CA -C N CA -C N CA C N CA CB SG N CA C +N [ impropers ] -C CA N H improper_X_X_N_X N C CA HA improper_X_X_C_X N C CA CB improper_N_A_C1_C CA +N C O improper_X_X_A_X CA SG CB HB1 improper_X_X_C_X CA SG CB HB2 improper_X_X_C_X [ CYSH ] [ atoms ] N N1 -0.333 0 H HN 0.333 0 CA C1 -0.119 1 HA H 0.119 1 CB C2 -0.238 2 HB1 H 0.119 2 HB2 H 0.119 2 SG SH -0.200 3 HG H 0.200 3 C Aprime 0.380 4 O O -0.380 4 [ bonds ] N H N CA CA HA CA CB CA C CB HB1 CB HB2 CB SG SG HG C O -C N [ dihedrals ] -CA -C N CA -C N CA C N CA CB SG CA CB SG HG N CA C +N [ impropers ] -C CA N H improper_X_X_N_X N C CA HA improper_X_X_C_X N C CA CB improper_N_A_C1_C CA +N C O improper_X_X_A_X CA SG CB HB1 improper_X_X_C_X CA SG CB HB2 improper_X_X_C_X [ CYH ] ; same as cysh [ atoms ] N N1 -0.333 0 H HN 0.333 0 CA C1 -0.119 1 HA H 0.119 1 CB C2 -0.238 2 HB1 H 0.119 2 HB2 H 0.119 2 SG SH -0.200 3 HG H 0.200 3 C Aprime 0.380 4 O O -0.380 4 [ bonds ] N H N CA CA HA CA CB CA C CB HB1 CB HB2 CB SG SG HG C O -C N [ dihedrals ] -CA -C N CA -C N CA C N CA CB SG CA CB SG HG N CA C +N [ impropers ] -C CA N H improper_X_X_N_X N C CA HA improper_X_X_C_X N C CA CB improper_N_A_C1_C CA +N C O improper_X_X_A_X CA SG CB HB1 improper_X_X_C_X CA SG CB HB2 improper_X_X_C_X [ GLN ] [ atoms ] N N1 -0.333 0 H HN 0.333 0 CA C1 -0.119 1 HA H 0.119 1 CB C2 -0.238 2 HB1 H 0.119 2 HB2 H 0.119 2 CG C2 -0.238 3 HG1 H 0.119 3 HG2 H 0.119 3 CD Aprime 0.380 4 OE1 O -0.380 4 NE2 N2 -0.666 5 HE21 HN 0.333 5 HE22 HN 0.333 5 C Aprime 0.380 6 O O -0.380 6 [ bonds ] N H N CA CA HA CA CB CA C CB HB1 CB HB2 CB CG CG HG1 CG HG2 CG CD CD OE1 CD NE2 NE2 HE21 NE2 HE22 C O -C N [ dihedrals ] -CA -C N CA -C N CA C N CA CB CG CA CB CG CD CB CG CD NE2 CG CD NE2 HE22 N CA C +N [ impropers ] -C CA N H improper_X_X_N_X N C CA HA improper_X_X_C_X N C CA CB improper_N_A_C1_C CA +N C O improper_X_X_A_X CA CG CB HB1 improper_X_X_C_X CA CG CB HB2 improper_X_X_C_X CB CD CG HG1 improper_X_X_C_X CB CD CG HG2 improper_X_X_C_X CG NE2 CD OE1 improper_X_X_A_X CD HE22 NE2 HE21 improper_X_X_N_X [ GLU ] [ atoms ] N N1 -0.333 0 H HN 0.333 0 CA C1 -0.119 1 HA H 0.119 1 CB C2 -0.238 2 HB1 H 0.119 2 HB2 H 0.119 2 CG C2 -0.238 3 HG1 H 0.119 3 HG2 H 0.119 3 CD Abis 0.840 4 OE1 Obis -0.920 4 OE2 Obis -0.920 4 C Aprime 0.380 5 O O -0.380 5 [ bonds ] N H N CA CA HA CA CB CA C CB HB1 CB HB2 CB CG CG HG1 CG HG2 CG CD CD OE1 CD OE2 C O -C N [ dihedrals ] -CA -C N CA -C N CA C N CA CB CG N CA C +N CA CB CG CD CB CG CD OE2 [ impropers ] -C CA N H improper_X_X_N_X N C CA HA improper_X_X_C_X N C CA CB improper_N_A_C1_C CA CG CB HB1 improper_X_X_C_X CA CG CB HB2 improper_X_X_C_X CA +N C O improper_X_X_A_X CB CD CG HG1 improper_X_X_C_X CB CD CG HG2 improper_X_X_C_X CG OE2 CD OE1 improper_X_X_A_X [ GLUH ] [ atoms ] N N1 -0.333 1 H HN 0.333 1 CA C1 -0.119 1 HA H 0.119 1 CB C2 -0.238 2 HB1 H 0.119 2 HB2 H 0.119 2 CG C2 -0.238 3 HG1 H 0.119 3 HG2 H 0.119 3 CD Aprime 0.380 4 OE1 O -0.380 4 OE2 OH -0.433 5 HE2 HO 0.433 5 C Aprime 0.380 6 O O -0.380 6 [ bonds ] N H N CA CA HA CA CB CA C CB HB1 CB HB2 CB CG CG HG1 CG HG2 CG CD CD OE1 CD OE2 OE2 HE2 C O -C N [ dihedrals ] -CA -C N CA -C N CA C N CA CB CG N CA C +N CA CB CG CD CB CG CD OE2 CG CD OE2 HE2 [ impropers ] -C CA N H improper_X_X_N_X N C CA HA improper_X_X_C_X N C CA CB improper_N_A_C1_C CA CG CB HB1 improper_X_X_C_X CA CG CB HB2 improper_X_X_C_X CB CD CG HG1 improper_X_X_C_X CB CD CG HG2 improper_X_X_C_X CG OE2 CD OE1 improper_X_X_A_X CA +N C O improper_X_X_A_X [ GLY ] [ atoms ] N N1 -0.333 0 H HN 0.333 0 CA C2 -0.238 1 HA1 H 0.119 1 HA2 H 0.119 1 C Aprime 0.380 2 O O -0.380 2 [ bonds ] N H N CA CA HA1 CA HA2 CA C C O -C N [ dihedrals ] -CA -C N CA -C N CA C N CA C +N [ impropers ] -C CA N H improper_X_X_N_X N C CA HA1 improper_X_X_C_X N C CA HA2 improper_X_X_C_X CA +N C O improper_X_X_A_X [ HISA ] ; A.K.A. HISD/HID [ atoms ] N N1 -0.333 0 H HN 0.333 0 CA C1 -0.119 1 HA H 0.119 1 CB C2 -0.238 2 HB1 H 0.119 2 HB2 H 0.119 2 CG A5 0.000 3 ND1 N1 -0.333 4 HD1 HN 0.333 4 CE1 A5 0.081 5 HE1 H 0.119 5 NE2 L5 -0.400 5 CD2 A5 0.081 5 HD2 H 0.119 5 C Aprime 0.380 6 O O -0.380 6 [ bonds ] N H N CA CA HA CA CB CA C CB HB1 CB HB2 CB CG CG ND1 CG CD2 ND1 HD1 ND1 CE1 CD2 HD2 CD2 NE2 CE1 HE1 CE1 NE2 C O -C N [ dihedrals ] -CA -C N CA -C N CA C N CA CB CG N CA C +N CA CB CG CD2 CB CG ND1 CE1 CG ND1 CE1 NE2 ND1 CE1 NE2 CD2 CE1 NE2 CD2 CG [ impropers ] -C CA N H improper_X_X_N_X N C CA HA improper_X_X_C_X N C CA CB improper_N_A_C1_C CA CG CB HB1 improper_X_X_C_X CA CG CB HB2 improper_X_X_C_X CB CD2 CG ND1 improper_X_X_A_X CG CE1 ND1 HD1 improper_X_X_N_X ND1 NE2 CE1 HE1 improper_X_X_A_X NE2 CG CD2 HD2 improper_X_X_A_X CA +N C O improper_X_X_A_X [ HID ] ; same as HISA [ atoms ] N N1 -0.333 0 H HN 0.333 0 CA C1 -0.119 1 HA H 0.119 1 CB C2 -0.238 2 HB1 H 0.119 2 HB2 H 0.119 2 CG A5 0.000 3 ND1 N1 -0.333 4 HD1 HN 0.333 4 CE1 A5 0.081 5 HE1 H 0.119 5 NE2 L5 -0.400 5 CD2 A5 0.081 5 HD2 H 0.119 5 C Aprime 0.380 6 O O -0.380 6 [ bonds ] N H N CA CA HA CA CB CA C CB HB1 CB HB2 CB CG CG ND1 CG CD2 ND1 HD1 ND1 CE1 CD2 HD2 CD2 NE2 CE1 HE1 CE1 NE2 C O -C N [ dihedrals ] -CA -C N CA -C N CA C N CA CB CG N CA C +N CA CB CG CD2 CB CG ND1 CE1 CG ND1 CE1 NE2 ND1 CE1 NE2 CD2 CE1 NE2 CD2 CG [ impropers ] -C CA N H improper_X_X_N_X N C CA HA improper_X_X_C_X N C CA CB improper_N_A_C1_C CA CG CB HB1 improper_X_X_C_X CA CG CB HB2 improper_X_X_C_X CB CD2 CG ND1 improper_X_X_A_X CG CE1 ND1 HD1 improper_X_X_N_X ND1 NE2 CE1 HE1 improper_X_X_A_X NE2 CG CD2 HD2 improper_X_X_A_X CA +N C O improper_X_X_A_X [ HIS1 ] Identical to HISA [ atoms ] N N1 -0.333 0 H HN 0.333 0 CA C1 -0.119 1 HA H 0.119 1 CB C2 -0.238 2 HB1 H 0.119 2 HB2 H 0.119 2 CG A5 0.000 3 ND1 N1 -0.333 4 HD1 HN 0.333 4 CE1 A5 0.081 5 HE1 H 0.119 5 NE2 L5 -0.400 5 CD2 A5 0.081 5 HD2 H 0.119 5 C Aprime 0.380 6 O O -0.380 6 [ bonds ] N H N CA CA HA CA CB CA C CB HB1 CB HB2 CB CG CG ND1 CG CD2 ND1 HD1 ND1 CE1 CD2 HD2 CD2 NE2 CE1 HE1 CE1 NE2 C O -C N [ dihedrals ] -CA -C N CA -C N CA C N CA CB CG N CA C +N CA CB CG CD2 CB CG ND1 CE1 CG ND1 CE1 NE2 ND1 CE1 NE2 CD2 CE1 NE2 CD2 CG [ impropers ] -C CA N H improper_X_X_N_X N C CA HA improper_X_X_C_X N C CA CB improper_N_A_C1_C CA CG CB HB1 improper_X_X_C_X CA CG CB HB2 improper_X_X_C_X CB CD2 CG ND1 improper_X_X_A_X CG CE1 ND1 HD1 improper_X_X_N_X ND1 NE2 CE1 HE1 improper_X_X_A_X NE2 CG CD2 HD2 improper_X_X_A_X CA +N C O improper_X_X_A_X [ HISB ] ; A.K.A. HISE/HIE [ atoms ] N N1 -0.333 0 H HN 0.333 0 CA C1 -0.119 1 HA H 0.119 1 CB C2 -0.238 2 HB1 H 0.119 2 HB2 H 0.119 2 CG A5 0.200 3 ND1 L5 -0.400 3 CE1 A5 0.081 3 HE1 H 0.119 3 NE2 N1 -0.333 4 HE2 HN 0.333 4 CD2 A5 -0.119 5 HD2 H 0.119 5 C Aprime 0.380 6 O O -0.380 6 [ bonds ] N H N CA CA HA CA CB CA C CB HB1 CB HB2 CB CG CG ND1 CG CD2 ND1 CE1 CD2 HD2 CD2 NE2 CE1 HE1 CE1 NE2 NE2 HE2 C O -C N [ dihedrals ] -CA -C N CA -C N CA C N CA CB CG N CA C +N CA CB CG CD2 CB CG ND1 CE1 CG ND1 CE1 NE2 ND1 CE1 NE2 CD2 CE1 NE2 CD2 CG [ impropers ] -C CA N H improper_X_X_N_X N C CA HA improper_X_X_C_X N C CA CB improper_N_A_C1_C CA CG CB HB1 improper_X_X_C_X CA CG CB HB2 improper_X_X_C_X CB CD2 CG ND1 improper_X_X_A_X ND1 NE2 CE1 HE1 improper_X_X_A_X CE1 CD2 NE2 HE2 improper_X_X_N_X NE2 CG CD2 HD2 improper_X_X_A_X CA +N C O improper_X_X_A_X [ HIE ] ; same as HISB [ atoms ] N N1 -0.333 0 H HN 0.333 0 CA C1 -0.119 1 HA H 0.119 1 CB C2 -0.238 2 HB1 H 0.119 2 HB2 H 0.119 2 CG A5 0.200 3 ND1 L5 -0.400 3 CE1 A5 0.081 3 HE1 H 0.119 3 NE2 N1 -0.333 4 HE2 HN 0.333 4 CD2 A5 -0.119 5 HD2 H 0.119 5 C Aprime 0.380 6 O O -0.380 6 [ bonds ] N H N CA CA HA CA CB CA C CB HB1 CB HB2 CB CG CG ND1 CG CD2 ND1 CE1 CD2 HD2 CD2 NE2 CE1 HE1 CE1 NE2 NE2 HE2 C O -C N [ dihedrals ] -CA -C N CA -C N CA C N CA CB CG N CA C +N CA CB CG CD2 CB CG ND1 CE1 CG ND1 CE1 NE2 ND1 CE1 NE2 CD2 CE1 NE2 CD2 CG [ impropers ] -C CA N H improper_X_X_N_X N C CA HA improper_X_X_C_X N C CA CB improper_N_A_C1_C CA CG CB HB1 improper_X_X_C_X CA CG CB HB2 improper_X_X_C_X CB CD2 CG ND1 improper_X_X_A_X ND1 NE2 CE1 HE1 improper_X_X_A_X CE1 CD2 NE2 HE2 improper_X_X_N_X NE2 CG CD2 HD2 improper_X_X_A_X CA +N C O improper_X_X_A_X [ HISH ] ; also known as HISP (or HIS+) [ atoms ] N N1 -0.333 1 H HN 0.333 1 CA C1 -0.119 1 HA H 0.119 1 CB C2 -0.238 2 HB1 H 0.119 2 HB2 H 0.119 2 CG A5 0.200 3 ND1 N1 -0.300 3 HD1 HN 0.375 3 CE1 A5 0.206 3 HE1 H 0.119 3 NE2 N1 -0.300 3 HE2 HN 0.375 3 CD2 A5 0.206 3 HD2 H 0.119 3 C Aprime 0.380 4 O O -0.380 4 [ bonds ] N H N CA CA HA CA CB CA C CB HB1 CB HB2 CB CG CG ND1 CG CD2 ND1 HD1 ND1 CE1 CD2 HD2 CD2 NE2 CE1 HE1 CE1 NE2 NE2 HE2 C O -C N [ dihedrals ] -CA -C N CA -C N CA C N CA CB CG N CA C +N CA CB CG CD2 CB CG ND1 CE1 CG ND1 CE1 NE2 ND1 CE1 NE2 CD2 CE1 NE2 CD2 CG [ impropers ] -C CA N H improper_X_X_N_X N C CA HA improper_X_X_C_X N C CA CB improper_N_A_C1_C CA CG CB HB1 improper_X_X_C_X CA CG CB HB2 improper_X_X_C_X CB CD2 CG ND1 improper_X_X_A_X CG CE1 ND1 HD1 improper_X_X_N_X ND1 NE2 CE1 HE1 improper_X_X_A_X CE1 CD2 NE2 HE2 improper_X_X_N_X NE2 CG CD2 HD2 improper_X_X_A_X CA +N C O improper_X_X_A_X [ HOH ] ; SPC and encad water have identical charges. ; Include encadwater.itp instead of spc.itp to use the flexible encad bonds/angles ; instead of the rigid SPC model. [ atoms ] OW OW -0.82 0 HW1 HW 0.41 0 HW2 HW 0.41 0 [ bonds ] OW HW1 OW HW2 [ ILE ] [ atoms ] N N1 -0.333 0 H HN 0.333 0 CA C1 -0.119 1 HA H 0.119 1 CB C1 -0.119 2 HB H 0.119 2 CG2 C3 -0.357 3 HG21 H 0.119 3 HG22 H 0.119 3 HG23 H 0.119 3 CG1 C2 -0.238 4 HG11 H 0.119 4 HG12 H 0.119 4 CD C3 -0.357 5 HD1 H 0.119 5 HD2 H 0.119 5 HD3 H 0.119 5 C Aprime 0.380 6 O O -0.380 6 [ bonds ] N H N CA CA HA CA CB CA C CB HB CB CG1 CB CG2 CG1 HG11 CG1 HG12 CG1 CD CG2 HG21 CG2 HG22 CG2 HG23 CD HD1 CD HD2 CD HD3 C O -C N [ dihedrals ] -CA -C N CA -C N CA C N CA CB CG1 N CA C +N CA CB CG2 HG23 CA CB CG1 CD CB CG1 CD HD3 [ impropers ] -C CA N H improper_X_X_N_X N C CA HA improper_X_X_C_X N C CA CB improper_N_A_C1_C CA CG1 CB CG2 improper_C1_C2_C1_C3 CA CG1 CB HB improper_X_X_C_X CB CD CG1 HG11 improper_X_X_C_X CB CD CG1 HG12 improper_X_X_C_X CG1 HD3 CD HD1 improper_X_X_C_X CG1 HD3 CD HD2 improper_X_X_C_X CB HG23 CG2 HG21 improper_X_X_C_X CB HG23 CG2 HG22 improper_X_X_C_X CA +N C O improper_X_X_A_X [ LEU ] [ atoms ] N N1 -0.333 0 H HN 0.333 0 CA C1 -0.119 1 HA H 0.119 1 CB C2 -0.238 2 HB1 H 0.119 2 HB2 H 0.119 2 CG C1 -0.119 3 HG H 0.119 3 CD1 C3 -0.357 4 HD11 H 0.119 4 HD12 H 0.119 4 HD13 H 0.119 4 CD2 C3 -0.357 5 HD21 H 0.119 5 HD22 H 0.119 5 HD23 H 0.119 5 C Aprime 0.380 6 O O -0.380 6 [ bonds ] N H N CA CA HA CA CB CA C CB HB1 CB HB2 CB CG CG HG CG CD1 CG CD2 CD1 HD11 CD1 HD12 CD1 HD13 CD2 HD21 CD2 HD22 CD2 HD23 C O -C N [ dihedrals ] -CA -C N CA -C N CA C N CA CB CG N CA C +N CA CB CG CD2 CB CG CD1 HD13 CB CG CD2 HD23 [ impropers ] -C CA N H improper_X_X_N_X N C CA HA improper_X_X_C_X N C CA CB improper_N_A_C1_C CA CG CB HB1 improper_X_X_C_X CA CG CB HB2 improper_X_X_C_X CB CD2 CG HG improper_X_X_C_X CB CD2 CG CD1 improper_X_X_C_X CG HD13 CD1 HD11 improper_X_X_C_X CG HD13 CD1 HD12 improper_X_X_C_X CG HD23 CD2 HD21 improper_X_X_C_X CG HD23 CD2 HD22 improper_X_X_C_X CA +N C O improper_X_X_A_X [ LYS ] ; non-protonated - see LYSH for the most common state. [ atoms ] N N1 -0.333 0 H HN 0.333 0 CA C1 -0.119 1 HA H 0.119 1 CB C2 -0.238 2 HB1 H 0.119 2 HB2 H 0.119 2 CG C2 -0.238 3 HG1 H 0.119 3 HG2 H 0.119 3 CD C2 -0.238 4 HD1 H 0.119 4 HD2 H 0.119 4 CE C2 -0.238 5 HE1 H 0.119 5 HE2 H 0.119 5 NZ N2 -0.666 6 HZ1 HN 0.333 6 HZ2 HN 0.333 6 C Aprime 0.380 7 O O -0.380 7 [ bonds ] N H N CA CA HA CA CB CA C CB HB1 CB HB2 CB CG CG HG1 CG HG2 CG CD CD HD1 CD HD2 CD CE CE HE1 CE HE2 CE NZ NZ HZ1 NZ HZ2 C O -C N [ dihedrals ] -CA -C N CA -C N CA C N CA CB CG N CA C +N CA CB CG CD CB CG CD CE CG CD CE NZ CD CE NZ HZ2 [ impropers ] -C CA N H improper_X_X_N_X N C CA HA improper_X_X_C_X N C CA CB improper_N_A_C1_C CA CG CB HB1 improper_X_X_C_X CA CG CB HB2 improper_X_X_C_X CB CD CG HG1 improper_X_X_C_X CB CD CG HG2 improper_X_X_C_X CG CE CD HD1 improper_X_X_C_X CG CE CD HD2 improper_X_X_C_X CD NZ CE HE1 improper_X_X_C_X CD NZ CE HE2 improper_X_X_C_X CE HZ2 NZ HZ1 improper_X_X_M_X CA +N C O improper_X_X_A_X [ LYSH ] [ atoms ] N N1 -0.333 0 H HN 0.333 0 CA C1 -0.119 1 HA H 0.119 1 CB C2 -0.238 2 HB1 H 0.119 2 HB2 H 0.119 2 CG C2 -0.238 3 HG1 H 0.119 3 HG2 H 0.119 3 CD C2 -0.238 4 HD1 H 0.119 4 HD2 H 0.119 4 CE C2 -0.238 5 HE1 H 0.119 5 HE2 H 0.119 5 NZ M3 -0.710 6 HZ1 HN 0.570 6 HZ2 HN 0.570 6 HZ3 HN 0.570 6 C Aprime 0.380 7 O O -0.380 7 [ bonds ] N H N CA CA HA CA CB CA C CB HB1 CB HB2 CB CG CG HG1 CG HG2 CG CD CD HD1 CD HD2 CD CE CE HE1 CE HE2 CE NZ NZ HZ1 NZ HZ2 NZ HZ3 C O -C N [ dihedrals ] -CA -C N CA -C N CA C N CA CB CG N CA C +N CA CB CG CD CB CG CD CE CG CD CE NZ CD CE NZ HZ3 [ impropers ] -C CA N H improper_X_X_N_X N C CA HA improper_X_X_C_X N C CA CB improper_N_A_C1_C CA CG CB HB1 improper_X_X_C_X CA CG CB HB2 improper_X_X_C_X CB CD CG HG1 improper_X_X_C_X CB CD CG HG2 improper_X_X_C_X CG CE CD HD1 improper_X_X_C_X CG CE CD HD2 improper_X_X_C_X CD NZ CE HE1 improper_X_X_C_X CD NZ CE HE2 improper_X_X_C_X CE HZ3 NZ HZ1 improper_X_X_M3_X CE HZ3 NZ HZ2 improper_X_X_M3_X CA +N C O improper_X_X_A_X [ MET ] [ atoms ] N N1 -0.333 0 H HN 0.333 0 CA C1 -0.119 1 HA H 0.119 1 CB C2 -0.238 2 HB1 H 0.119 2 HB2 H 0.119 2 CG C2 -0.238 3 HG1 H 0.119 3 HG2 H 0.119 3 SD S 0.000 4 CE C3 -0.357 5 HE1 H 0.119 5 HE2 H 0.119 5 HE3 H 0.119 5 C Aprime 0.380 6 O O -0.380 6 [ bonds ] N H N CA CA HA CA CB CA C CB HB1 CB HB2 CB CG CG HG1 CG HG2 CG SD SD CE CE HE1 CE HE2 CE HE3 C O -C N [ dihedrals ] -CA -C N CA -C N CA C N CA CB CG N CA C +N CA CB CG SD CB CG SD CE CG SD CE HE3 [ impropers ] -C CA N H improper_X_X_N_X N C CA HA improper_X_X_C_X N C CA CB improper_N_A_C1_C CA CG CB HB1 improper_X_X_C_X CA CG CB HB2 improper_X_X_C_X CB SD CG HG1 improper_X_X_C_X CB SD CG HG2 improper_X_X_C_X SD HE3 CE HE1 improper_X_X_C_X SD HE3 CE HE2 improper_X_X_C_X CA +N C O improper_X_X_A_X [ NAC ] ; metylamide, a.k.a NMA. [ atoms ] N N1 -0.333 1 H HN 0.333 1 CH3 C3 -0.357 2 HH31 H 0.119 2 HH32 H 0.119 2 HH33 H 0.119 2 [ bonds ] N H N CH3 CH3 HH31 CH3 HH32 CH3 HH33 -C N [ dihedrals ] -CA -C N CH3 -C N CH3 HH33 [ impropers ] -C CH3 N H improper_X_X_N_X N HH33 CH3 HH31 improper_X_X_C_X N HH33 CH3 HH32 improper_X_X_C_X [ NH2 ] [ atoms ] N N2 -0.666 1 H1 HN 0.333 1 H2 HN 0.333 1 [ bonds ] -C N N H1 N H2 [ dihedrals ] -CA -C N H2 [ impropers ] -C H2 N H1 improper_X_X_N_X [ NHE ] ; same as NH2 [ atoms ] N N2 -0.666 1 H1 HN 0.333 1 H2 HN 0.333 1 [ bonds ] -C N N H1 N H2 [ dihedrals ] -CA -C N H2 [ impropers ] -C H2 N H1 improper_X_X_N_X [ PHE ] [ atoms ] N N1 -0.333 0 H HN 0.333 0 CA C1 -0.119 1 HA H 0.119 1 CB C2 -0.238 2 HB1 H 0.119 2 HB2 H 0.119 2 CG A6 0.000 3 CD1 A6 -0.119 4 HD1 H 0.119 4 CE1 A6 -0.119 5 HE1 H 0.119 5 CZ A6 -0.119 6 HZ H 0.119 6 CE2 A6 -0.119 7 HE2 H 0.119 7 CD2 A6 -0.119 8 HD2 H 0.119 8 C Aprime 0.380 9 O O -0.380 9 [ bonds ] N H N CA CA HA CA CB CA C CB HB1 CB HB2 CB CG CG CD1 CG CD2 CD1 HD1 CD1 CE1 CD2 HD2 CD2 CE2 CE1 HE1 CE1 CZ CE2 HE2 CE2 CZ CZ HZ C O -C N [ dihedrals ] -CA -C N CA -C N CA C N CA CB CG N CA C +N CA CB CG CD2 CB CG CD1 CE1 CB CG CD2 CE2 CG CD1 CE1 CZ CD1 CE1 CZ CE2 CE1 CZ CE2 CD2 CZ CE2 CD2 CG [ impropers ] -C CA N H improper_X_X_N_X N C CA HA improper_X_X_C_X N C CA CB improper_N_A_C1_C CA CG CB HB1 improper_X_X_C_X CA CG CB HB2 improper_X_X_C_X CB CD2 CG CD1 improper_X_X_A_X CG CE1 CD1 HD1 improper_X_X_A_X CD1 CZ CE1 HE1 improper_X_X_A_X CE1 CE2 CZ HZ improper_X_X_A_X CE2 CG CD2 HD2 improper_X_X_A_X CZ CD2 CE2 HE2 improper_X_X_A_X CA +N C O improper_X_X_A_X [ PRO ] [ atoms ] N N 0.000 0 CA C1 -0.119 1 HA H 0.119 1 CB CP -0.238 2 HB1 H 0.119 2 HB2 H 0.119 2 CG CP -0.238 3 HG1 H 0.119 3 HG2 H 0.119 3 CD CP -0.238 4 HD1 H 0.119 4 HD2 H 0.119 4 C Aprime 0.380 5 O O -0.380 5 [ bonds ] N CA CA HA CA CB CA C CB HB1 CB HB2 CB CG CG HG1 CG HG2 CG CD CD HD1 CD HD2 CD N C O -C N [ dihedrals ] -CA -C N CD -C N CA C N CA CB CG N CA C +N CA CB CG CD CB CG CD N [ impropers ] -C CA N H improper_X_X_N_X N C CA HA improper_X_X_C_X N C CA CB improper_N_A_C1_C CA CG CB HB1 improper_X_X_C_X CA CG CB HB2 improper_X_X_C_X CB CD CG HG1 improper_X_X_C_X CB CD CG HG2 improper_X_X_C_X CG N CD HD1 improper_X_X_C_X CG N CD HD2 improper_X_X_C_X -C CD N CA improper_X_X_N_X CA +N C O improper_X_X_A_X [ SER ] [ atoms ] N N1 -0.333 0 H HN 0.333 0 CA C1 -0.119 1 HA H 0.119 1 CB C2 -0.238 2 HB1 H 0.119 2 HB2 H 0.119 2 OG OH -0.433 3 HG HO 0.433 3 C Aprime 0.380 4 O O -0.380 4 [ bonds ] N H N CA CA HA CA CB CA C CB HB1 CB HB2 CB OG OG HG C O -C N [ dihedrals ] -CA -C N CA -C N CA C N CA CB OG N CA C +N CA CB OG HG [ impropers ] -C CA N H improper_X_X_N_X N C CA HA improper_X_X_C_X N C CA CB improper_N_A_C1_C CA OG CB HB1 improper_X_X_C_X CA OG CB HB2 improper_X_X_C_X CA +N C O improper_X_X_A_X [ THR ] [ atoms ] N N1 -0.333 0 H HN 0.333 0 CA C1 -0.119 1 HA H 0.119 1 CB C1 -0.119 2 HB H 0.119 2 OG1 OH -0.433 3 HG1 HO 0.433 3 CG2 C3 -0.357 4 HG21 H 0.119 4 HG22 H 0.119 4 HG23 H 0.119 4 C Aprime 0.380 5 O O -0.380 5 [ bonds ] N H N CA CA HA CA CB CA C CB HB CB OG1 CB CG2 OG1 HG1 CG2 HG21 CG2 HG22 CG2 HG23 C O -C N [ dihedrals ] -CA -C N CA -C N CA C N CA CB CG2 N CA C +N CA CB OG1 HG1 CA CB CG2 HG23 [ impropers ] -C CA N H improper_X_X_N_X N C CA HA improper_X_X_C_X N C CA CB improper_N_A_C1_C CA CG2 CB OG1 improper_X_X_C_X CA CG2 CB HB improper_X_X_C_X CB HG23 CG2 HG21 improper_X_X_C_X CB HG23 CG2 HG22 improper_X_X_C_X CA +N C O improper_X_X_A_X [ TRP ] [ atoms ] N N1 -0.333 0 H HN 0.333 0 CA C1 -0.119 1 HA H 0.119 1 CB C2 -0.238 2 HB1 H 0.119 2 HB2 H 0.119 2 CG A5 0.000 3 CD1 A5 -0.119 4 HD1 H 0.119 4 NE1 N1 -0.333 5 HE1 HN 0.333 5 CE2 A7 0.000 6 CZ2 A6 -0.119 7 HZ2 H 0.119 7 CH2 A6 -0.119 8 HH2 H 0.119 8 CZ3 A6 -0.119 9 HZ3 H 0.119 9 CE3 A6 -0.119 10 HE3 H 0.119 10 CD2 A7 0.000 11 C Aprime 0.380 12 O O -0.380 12 [ bonds ] N H N CA CA HA CA CB CA C CB HB1 CB HB2 CB CG CG CD1 CG CD2 CD1 HD1 CD1 NE1 CD2 CE2 CD2 CE3 NE1 HE1 NE1 CE2 CE2 CZ2 CE3 HE3 CE3 CZ3 CZ2 HZ2 CZ2 CH2 CZ3 HZ3 CZ3 CH2 CH2 HH2 C O -C N [ dihedrals ] -CA -C N CA -C N CA C N CA CB CG N CA C +N CA CB CG CD2 CB CG CD1 NE1 CG CD1 NE1 CE2 CD1 NE1 CE2 CD2 NE1 CE2 CD2 CE3 NE1 CE2 CZ2 CH2 CE2 CZ2 CH2 CZ3 CZ2 CH2 CZ3 CE3 CH2 CZ3 CE3 CD2 CZ3 CE3 CD2 CE2 CB CG CD2 CE3 [ impropers ] -C CA N H improper_X_X_N_X CA +N C O improper_X_X_A_X N C CA CB improper_N_A_C1_C N C CA HA improper_X_X_C_X CA CG CB HB1 improper_X_X_C_X CA CG CB HB2 improper_X_X_C_X CB CD2 CG CD1 improper_X_X_A_X CG NE1 CD1 HD1 improper_X_X_A_X CD1 CE2 NE1 HE1 improper_X_X_N_X NE1 CD2 CE2 CZ2 improper_X_X_A_X CE2 CH2 CZ2 HZ2 improper_X_X_A_X CZ2 CZ3 CH2 HH2 improper_X_X_A_X CH2 CE3 CZ3 HZ3 improper_X_X_A_X CZ3 CD2 CE3 HE3 improper_X_X_A_X CG CD2 CE2 CE3 improper_X_X_A_X [ TYR ] [ atoms ] N N1 -0.333 0 H HN 0.333 0 CA C1 -0.119 1 HA H 0.119 1 CB C2 -0.238 2 HB1 H 0.119 2 HB2 H 0.119 2 CG A6 0.000 3 CD1 A6 -0.119 4 HD1 H 0.119 4 CE1 A6 -0.119 5 HE1 H 0.119 5 CZ A6 0.000 6 OH OH -0.433 7 HH HO 0.433 7 CE2 A6 -0.119 8 HE2 H 0.119 8 CD2 A6 -0.119 9 HD2 H 0.119 9 C Aprime 0.380 10 O O -0.380 10 [ bonds ] N H N CA CA HA CA CB CA C CB HB1 CB HB2 CB CG CG CD1 CG CD2 CD1 HD1 CD1 CE1 CD2 HD2 CD2 CE2 CE1 HE1 CE1 CZ CE2 HE2 CE2 CZ CZ OH OH HH C O -C N [ dihedrals ] -CA -C N CA -C N CA C N CA CB CG N CA C +N CA CB CG CD2 CB CG CD1 CE1 CB CG CD2 CE2 CG CD1 CE1 CZ CD1 CE1 CZ CE2 CE1 CZ OH HO CE1 CZ CE2 CD2 CZ CE2 CD2 CG [ impropers ] -C CA N H improper_X_X_N_X N C CA HA improper_X_X_C_X N C CA CB improper_N_A_C1_C CA CG CB HB1 improper_X_X_C_X CA CG CB HB2 improper_X_X_C_X CB CD2 CG CD1 improper_X_X_A_X CG CE1 CD1 HD1 improper_X_X_A_X CD1 CZ CE1 HE1 improper_X_X_A_X CE1 CE2 CZ OH improper_X_X_A_X CE2 CG CD2 HD2 improper_X_X_A_X CZ CD2 CE2 HE2 improper_X_X_A_X CA +N C O improper_X_X_A_X [ VAL ] [ atoms ] N N1 -0.333 0 H HN 0.333 0 CA C1 -0.119 1 HA H 0.119 1 CB C1 -0.119 2 HB H 0.119 2 CG1 C3 -0.357 3 HG11 H 0.119 3 HG12 H 0.119 3 HG13 H 0.119 3 CG2 C3 -0.357 4 HG21 H 0.119 4 HG22 H 0.119 4 HG23 H 0.119 4 C Aprime 0.380 5 O O -0.380 5 [ bonds ] N H N CA CA HA CA CB CA C CB HB CB CG1 CB CG2 CG1 HG11 CG1 HG12 CG1 HG13 CG2 HG21 CG2 HG22 CG2 HG23 C O -C N [ dihedrals ] -CA -C N CA -C N CA C N CA CB CG2 N CA C +N CA CB CG2 HG23 CA CB CG1 HG13 [ impropers ] -C CA N H improper_X_X_N_X N C CA HA improper_X_X_C_X N C CA CB improper_N_A_C1_C CA CG2 CB HB improper_X_X_C_X CA CG2 CB CG1 improper_X_X_C_X CB HG13 CG1 HG11 improper_X_X_C_X CB HG13 CG1 HG12 improper_X_X_C_X CB HG23 CG2 HG21 improper_X_X_C_X CB HG23 CG2 HG22 improper_X_X_C_X CA +N C O improper_X_X_A_X [ CL ] [ atoms ] CL CL -1.000 0 [ NA ] [ atoms ] NA NA 1.000 0 [ FE ] [ atoms ] FE FE 2.000 0 [ Ar ] [ atoms ] AR AR 0.000 0