+++ /dev/null
-[ None ]
-
-[ COO- ]
-[ replace ]
-C C Abis 12.011 0.84
-O O1 Obis 15.9994 -0.92
-OXT O2 Obis 15.9994 -0.92
-[ add ]
-2 8 O C CA N
- Obis 15.9994 -0.92
-[ dihedrals ]
-N CA C O2
-[ impropers ]
-CA O2 C O1 improper_X_X_A_X
-N C CA CB improper_X_X_C_X
-
-[ Gly-COO- ]
-[ replace ]
-C C Abis 12.011 0.84
-O O Obis 15.9994 -0.92
-OXT O2 Obis 15.9994 -0.92
-[ add ]
-2 8 O C CA N
- Obis 15.9994 -0.92
-[ dihedrals ]
-N CA C O2
-[ impropers ]
-CA O2 C O1 improper_X_X_A_X
-
-[ COOH ]
-[ replace ]
-C C Aprime 12.011 0.38
-O O OH 15.9994 -0.38
-OXT OT O 15.9994 -0.433
-[ add ]
-1 2 OT C CA N
- O 15.9994 -0.433
-1 2 HO O C CA
- HO 1.008 0.433
-[ dihedrals ]
-N CA C O
-[ impropers ]
-OT CA C O improper_X_X_A_X
-
+++ /dev/null
-ACE 1
-3 4 HH3 CH3 C O
-ALA 3
-1 1 H N -C CA
-1 5 HA CA N C CB
-3 4 HB CB CA N
-ARG 8
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-2 6 HG CG CD CB
-2 6 HD CD NE CG
-1 1 HE NE CD CZ
-2 3 HH1 NH1 CZ NE
-2 3 HH2 NH2 CZ NE
-ARGN 8
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-2 6 HG CG CD CB
-2 6 HD CD NE CG
-1 1 HE NE CD CZ
-1 2 HH1 NH1 CZ NE
-2 3 HH2 NH2 CZ NE
-ASN 4
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-2 3 HD2 ND2 CG CB
-ASP 3
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-ASPH 4
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-1 2 HD2 OD2 CG CB
-CYS2 3
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB SG CA
-CYSH 4
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB SG CA
-1 2 HG SG CB CA
-GLN 5
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-2 6 HG CG CD CB
-2 3 HE2 NE2 CD CG
-GLU 4
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-2 6 HG CG CD CB
-GLUH 5
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-2 6 HG CG CD CB
-1 2 HE2 OE2 CD CG
-GLY 2
-1 1 H N -C CA
-2 6 HA CA C N
-HIS1 6
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-1 1 HD2 CD2 CG NE2
-1 1 HE1 CE1 ND1 NE2
-1 1 HD1 ND1 CG CE1
-HISA 6
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-1 1 HD2 CD2 CG NE2
-1 1 HE1 CE1 ND1 NE2
-1 1 HD1 ND1 CG CE1
-HISB 6
-1 1 H N -C CA
-2 6 HB CB CG CA
-1 5 HA CA N C CB
-1 1 HE2 NE2 CE1 CD2
-1 1 HD2 CD2 CG NE2
-1 1 HE1 CE1 ND1 NE2
-HISH 7
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-1 1 HD2 CD2 CG NE2
-1 1 HE1 CE1 ND1 NE2
-1 1 HD1 ND1 CG CE1
-1 1 HE2 NE2 CE1 CD2
-HOH 1
-2 7 HW OW
-ILE 6
-1 1 H N -C CA
-1 5 HA CA N C CB
-1 5 HB CB CA CG1 CG2
-2 6 HG1 CG1 CD CB
-3 4 HG2 CG2 CB CA
-3 4 HD CD CG1 CB
-LEU 6
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-1 5 HG CG CB CD1 CD2
-3 4 HD1 CD1 CG CB
-3 4 HD2 CD2 CG CB
-LYS 7
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-2 6 HG CG CD CB
-2 6 HD CD CE CG
-2 6 HE CE NZ CD
-2 4 HZ NZ CE CD
-LYSH 7
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-2 6 HG CG CD CB
-2 6 HD CD CE CG
-2 6 HE CE NZ CD
-3 4 HZ NZ CE CD
-MET 5
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-2 6 HG CG SD CB
-3 4 HE CE SD CG
-NAC 2
-1 1 H N -C CA
-3 4 HA CA N -C
-NH2 1
-2 3 H N -C -CA
-PHE 8
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-1 1 HD1 CD1 CG CE1
-1 1 HD2 CD2 CG CE2
-1 1 HE1 CE1 CD1 CZ
-1 1 HE2 CE2 CD2 CZ
-1 1 HZ CZ CE1 CE2
-PRO 4
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-2 6 HG CG CD CB
-2 6 HD CD N CG
-SER 4
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB OG CA
-1 2 HG OG CB CA
-THR 5
-1 1 H N -C CA
-1 5 HA CA N C CB
-1 5 HB CB CA OG1 CG2
-1 2 HG1 OG1 CB CA
-3 4 HG2 CG2 CB CA
-TRP 9
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-1 1 HD1 CD1 NE1 CG
-1 1 HE1 NE1 CD1 CE2
-1 1 HE3 CE3 CD2 CZ3
-1 1 HZ3 CZ3 CE3 CH2
-1 1 HH2 CH2 CZ3 CZ2
-1 1 HZ2 CZ2 CE2 CH2
-TYR 8
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-1 1 HD1 CD1 CG CE1
-1 1 HD2 CD2 CG CE2
-1 1 HE1 CE1 CD1 CZ
-1 1 HE2 CE2 CD2 CZ
-1 2 HH OH CZ CE1
-VAL 5
-1 1 H N -C CA
-1 5 HA CA N C CB
-1 5 HB CB CA CG1 CG2
-3 4 HG1 CG1 CB CA
-3 4 HG2 CG2 CB CA
+++ /dev/null
-[ None ]
-
-[ NH3+ ]
-[ replace ]
-N M3 14.0067 -0.71
-[ add ]
-3 4 H N CA C
- HN 1.008 0.57
-[ delete ]
-H
-[ dihedrals ]
-H1 N CA C
-[ impropers ]
-H1 CA N H2 improper_X_X_M3_X
-H1 CA N H3 improper_X_X_M3_X
-
-[ NH2 ]
-[ replace ]
-N N2 14.0067 -0.666
-[ add ]
-2 4 H N CA C
- HN 1.008 0.333
-[ delete ]
-H
-[ dihedrals ]
-H1 N CA C
-[ impropers ]
-H1 CA N H2 improper_X_X_M_X
-
-[ PRO-NH2+ ]
-[ replace ]
-N N2 14.0067 -0.14
-[ add ]
-2 4 H N CA C
- HN 1.008 0.57
-[ dihedrals ]
-H1 N CA C
-[ impropers ]
-H1 CA N H2 improper_X_X_M_X
-
-[ PRO-NH ]
-[ replace ]
-N N1 14.0067 -0.333
-[ add ]
-1 4 H N CA C
- HN 1.008 0.333
-[ dihedrals ]
-H1 N CA C
-
+++ /dev/null
-; rtp residue to rtp building block table
-;GMX Force-field
-CYS CYSH
-HISD HISA
-HISE HISB
-LYS LYSH
-LYSN LYS
+++ /dev/null
-;
-; 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 ]
-; Column 1 : default bondtype
-; Column 2 : default angletype
-; Column 3 : default proper dihedraltype
-; Column 4 : default improper dihedraltype
-; Column 5 : This controls the generation of dihedrals from the bonding.
-; All possible dihedrals are generated automatically. A value of
-; 1 here means that all these are retained. A value of
-; 0 here requires generated dihedrals be removed if
-; * there are any dihedrals on the same central atoms
-; specified in the residue topology, or
-; * there are other identical generated dihedrals
-; sharing the same central atoms, or
-; * there are other generated dihedrals sharing the
-; same central bond that have fewer hydrogen atoms
-; Column 6 : number of neighbors to exclude from non-bonded interactions
-; Column 7 : 1 = generate 1,4 interactions between pairs of hydrogen atoms
-; 0 = do not generate such
-; Column 8 : 1 = remove proper dihedrals if found centered on the same
-; bond as an improper dihedral
-; 0 = do not generate such
-; bonds angles dihedrals impropers all_dihedrals nrexcl bHH14 bRemoveDih
- 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 CD 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
-
+++ /dev/null
- H 1.008 ; Hydrogen bound to carbon
- O 15.9994 ; Oxygen
- N 14.0067 ; Trivalent nitrogen
- N1 14.0067 ; Trivalent nitrogen
- N2 14.0067 ; Trivalent nitrogen
- C1 12.011 ; Aliphatic carbon
- C2 12.011 ; Aliphatic carbon
- C3 12.011 ; Aliphatic carbon
- CP 12.011 ; Aliphatic carbon
- A6 12.011 ; Aromatic carbon
- A5 12.011 ; Aromatic carbon
- A7 12.011 ; Aromatic carbon
- Aprime 12.011 ; Aromatic carbon
- Abis 12.011 ; Aromatic carbon
- L5 14.0067 ; Acceptor nitrogen
- L6 14.0067 ; Acceptor nitrogen
- P 30.9738 ; Phosphorus
- OH 15.9994 ; Divalent oxygen
- O2 15.9994 ; Divalent oxygen
- OR 15.9994 ; Divalent oxygen
- S 32.060 ; Sulphur not bound to hydrogen
- SH 32.060 ; Sulphur with bound hydrogen
- M1 14.0067 ; Charged nitrogen
- M2 14.0067 ; Charged nitrogen
- M3 14.0067 ; Charged nitrogen
- HN 1.008 ; Polar hydrogen
- HO 1.008 ; Polar hydrogen
- HW 1.008 ; Water hydrogen
- CL 35.453 ; Chloride ion
- Obis 15.9994 ; Charged oxygen
- OP 15.9994 ; Charged oxygen
- R 14.0067 ; Heme nitrogen
- W 14.0067 ; Heme nitrogen
- Y 12.011 ; Heme carbon
- Z 12.011 ; Heme carbon
- FE 55.847 ; Heme Iron
- OF 15.9994 ; Heme oxygen
- OW 15.9994 ; Water oxygen
- AR 39.948 ; Argon
- NA 22.9898 ; Sodium
- MCH3 0 ; Dummy
- MNH3 0 ; Dummy
- MW 0 ; Dummy
+++ /dev/null
-;
-; f3c water for use with the Encad force fields.
-;
-
-[ moleculetype ]
-; molname nrexcl
-SOL 2
-
-#ifdef _FF_ENCAD
-[ atoms ]
-; nr type resnr residue atom cgnr charge mass
- 1 OW 1 SOL OW 1 -0.82
- 2 HW 1 SOL HW1 1 0.41
- 3 HW 1 SOL HW2 1 0.41
-
-[ bonds ]
-; i j funct length force.c.
-1 2 1 0.1 209200
-1 3 1 0.1 209200
-
-[ angles ]
-; i j k funct angle force.c.
-2 1 3 1 109.47 502.08
-#endif
-
-
+++ /dev/null
-[ bondtypes ]
- ; i j func b0 kb
- OW HW 1 0.10000 209200.0
- OH HO 1 0.10000 209200.0
- N1 HN 1 0.10000 209200.0
- N2 HN 1 0.10000 209200.0
- C1 H 1 0.10900 209200.0
- C2 H 1 0.10900 209200.0
- C3 H 1 0.10900 209200.0
- CP H 1 0.10900 209200.0
- C1 O 1 0.14370 209200.0
- C2 O2 1 0.14370 209200.0
- C2 OR 1 0.14370 209200.0
- C1 OH 1 0.14390 209200.0
- C2 OH 1 0.14390 209200.0
- C3 OH 1 0.14390 209200.0
- C1 N 1 0.14670 209200.0
- C1 N1 1 0.14670 209200.0
- C1 N2 1 0.14670 209200.0
- C2 N 1 0.14670 209200.0
- C2 N1 1 0.14670 209200.0
- C2 N2 1 0.14670 209200.0
- C3 N 1 0.14670 209200.0
- C3 N1 1 0.14670 209200.0
- C3 N2 1 0.14670 209200.0
- CP N 1 0.14670 209200.0
- CP N1 1 0.14670 209200.0
- CP N2 1 0.14670 209200.0
- C1 M1 1 0.14720 209200.0
- C1 M2 1 0.14720 209200.0
- C1 M3 1 0.14720 209200.0
- C2 M1 1 0.14720 209200.0
- C2 M2 1 0.14720 209200.0
- C2 M3 1 0.14720 209200.0
- C3 M1 1 0.14720 209200.0
- C3 M2 1 0.14720 209200.0
- C3 M3 1 0.14720 209200.0
- C1 C1 1 0.15250 209200.0
- C1 C2 1 0.15250 209200.0
- C1 C3 1 0.15250 209200.0
- C2 C2 1 0.15250 209200.0
- C2 C3 1 0.15250 209200.0
- C3 C3 1 0.15250 209200.0
- CP CP 1 0.15190 209200.0
- C1 CP 1 0.14980 209200.0
- A6 H 1 0.10900 209200.0
- A5 H 1 0.10900 209200.0
- A7 H 1 0.10900 209200.0
- A6 C1 1 0.15260 209200.0
- A6 C2 1 0.15260 209200.0
- A6 C3 1 0.15260 209200.0
- A6 OH 1 0.13780 209200.0
- A7 C1 1 0.15260 209200.0
- A7 C2 1 0.15260 209200.0
- A7 C3 1 0.15260 209200.0
- Aprime C1 1 0.15260 209200.0
- Abis C1 1 0.15260 209200.0
- Aprime C2 1 0.15260 209200.0
- Aprime C3 1 0.15260 209200.0
- Abis C2 1 0.15260 209200.0
- Abis C3 1 0.15260 209200.0
- Aprime O 1 0.12360 418400.0
- Aprime OH 1 0.12360 418400.0
- Abis Obis 1 0.12230 418400.0
- Aprime N 1 0.13220 418400.0
- Aprime N1 1 0.13220 418400.0
- Aprime N2 1 0.13220 418400.0
- A5 N 1 0.13340 418400.0
- A5 N1 1 0.13340 418400.0
- A5 N2 1 0.13340 418400.0
- A5 C1 1 0.15160 209200.0
- A5 C2 1 0.15160 209200.0
- A5 C3 1 0.15160 209200.0
- A5 A5 1 0.13760 418400.0
- A5 A7 1 0.14510 418400.0
- A5 L5 1 0.13340 418400.0
- A6 O 1 0.12280 418400.0
- A6 O2 1 0.12280 418400.0
- A6 OR 1 0.12280 418400.0
- A6 A6 1 0.13890 418400.0
- A6 A7 1 0.14110 418400.0
- A6 M1 1 0.13350 418400.0
- A6 M2 1 0.13350 418400.0
- A6 M3 1 0.13350 418400.0
- A7 N 1 0.13670 418400.0
- A7 N2 1 0.13670 418400.0
- A7 N1 1 0.13430 418400.0
- A7 A7 1 0.13640 418400.0
- SH H 1 0.13300 209200.0
- S C2 1 0.18080 209200.0
- S C3 1 0.18080 209200.0
- SH C2 1 0.18080 209200.0
- S S 1 0.20150 209200.0
- M1 HN 1 0.10000 209200.0
- M2 HN 1 0.10000 209200.0
- M3 HN 1 0.10000 209200.0
- A6 N 1 0.13550 418400.0
- A6 N1 1 0.13550 418400.0
- A6 N2 1 0.13550 418400.0
- A6 L5 1 0.13550 418400.0
- A6 L6 1 0.13550 418400.0
- A7 L5 1 0.13670 418400.0
- A7 L6 1 0.13670 418400.0
- P OP 1 0.14800 418400.0
- P O2 1 0.15940 209200.0
- Y A6 1 0.13960 418400.0
- Y Aprime 1 0.13960 418400.0
- Y R 1 0.13840 418400.0
- Y W 1 0.13840 418400.0
- Z C2 1 0.15170 209200.0
- Z C3 1 0.15170 209200.0
- Z A6 1 0.14900 418400.0
- Z Aprime 1 0.14900 418400.0
- Z Y 1 0.14440 418400.0
- Z Z 1 0.13570 418400.0
- FE N 1 0.19800 58576.0
- FE N1 1 0.19800 58576.0
- FE N2 1 0.19800 58576.0
- FE W 1 0.19800 58576.0
- OF FE 1 0.16320 58576.0 ; iron-oxygen bond
- OF OF 1 0.12240 418400.0
-
-;[ constrainttypes ]
-
-[ angletypes ]
- ; i j k func th0 cth
- HW OW HW 1 109.47 502.08
- C1 OH HO 1 110.00 502.08
- C2 OH HO 1 110.00 502.08
- C3 OH HO 1 110.00 502.08
- Aprime OH HO 1 110.00 502.08
- A6 OH HO 1 110.00 502.08
- C1 C1 Abis 1 110.10 502.08
- C2 C1 Abis 1 110.10 502.08
- C3 C1 Abis 1 110.10 502.08
- HN N2 HN 1 120.00 502.08
- CP N1 HN 1 119.50 502.08
- CP N2 HN 1 119.50 502.08
- C1 N1 HN 1 119.50 502.08
- C1 N2 HN 1 119.50 502.08
- C2 N1 HN 1 119.50 502.08
- C2 N2 HN 1 119.50 502.08
- C3 N1 HN 1 119.50 502.08
- C3 N2 HN 1 119.50 502.08
- A6 N1 HN 1 119.60 502.08
- A6 N2 HN 1 119.60 502.08
- A5 N1 HN 1 119.60 502.08
- A5 N2 HN 1 119.60 502.08
- A7 N1 HN 1 119.60 502.08
- A7 N2 HN 1 119.60 502.08
- Aprime N1 HN 1 119.60 502.08
- Aprime N2 HN 1 119.60 502.08
- N2 Aprime N2 1 113.00 502.08
- C2 Aprime C3 1 118.00 502.08
- C1 N C1 1 112.40 502.08
- C1 N C2 1 112.40 502.08
- C1 N C3 1 112.40 502.08
- C1 N1 CP 1 112.40 502.08
- C1 N1 C1 1 112.40 502.08
- C1 N1 C2 1 112.40 502.08
- C1 N1 C3 1 112.40 502.08
- C1 N2 CP 1 112.40 502.08
- C1 N2 C1 1 112.40 502.08
- C1 N2 C2 1 112.40 502.08
- C1 N2 C3 1 112.40 502.08
- C2 N C2 1 112.40 502.08
- C2 N C3 1 112.40 502.08
- C2 N1 C2 1 112.40 502.08
- C2 N1 C3 1 112.40 502.08
- C2 N2 C2 1 112.40 502.08
- C2 N2 C3 1 112.40 502.08
- C3 N C3 1 112.40 502.08
- C3 N1 C3 1 112.40 502.08
- C3 N2 C3 1 112.40 502.08
- C1 N CP 1 112.40 502.08
- A6 N C1 1 121.30 502.08
- A6 N C2 1 121.30 502.08
- A6 N C3 1 121.30 502.08
- A6 N1 C1 1 121.30 502.08
- A6 N1 C2 1 121.30 502.08
- A6 N1 C3 1 121.30 502.08
- A6 N2 C1 1 121.30 502.08
- A6 N2 C2 1 121.30 502.08
- A6 N2 C3 1 121.30 502.08
- A5 N C1 1 121.30 502.08
- A5 N C2 1 121.30 502.08
- A5 N C3 1 121.30 502.08
- A5 N1 C1 1 121.30 502.08
- A5 N1 C2 1 121.30 502.08
- A5 N1 C3 1 121.30 502.08
- A5 N2 C1 1 121.30 502.08
- A5 N2 C2 1 121.30 502.08
- A5 N2 C3 1 121.30 502.08
- A7 N C1 1 121.30 502.08
- A7 N C2 1 121.30 502.08
- A7 N C3 1 121.30 502.08
- A7 N1 C1 1 121.30 502.08
- A7 N1 C2 1 121.30 502.08
- A7 N1 C3 1 121.30 502.08
- A7 N2 C1 1 121.30 502.08
- A7 N2 C2 1 121.30 502.08
- A7 N2 C3 1 121.30 502.08
- Aprime N C1 1 121.30 502.08
- Aprime N C2 1 121.30 502.08
- Aprime N C3 1 121.30 502.08
- Aprime N1 C1 1 121.30 502.08
- Aprime N1 C2 1 121.30 502.08
- Aprime N1 C3 1 121.30 502.08
- Aprime N2 C1 1 121.30 502.08
- Aprime N2 C2 1 121.30 502.08
- Aprime N2 C3 1 121.30 502.08
- A5 N A5 1 108.00 1004.16
- A5 N1 A5 1 108.00 1004.16
- A5 N2 A5 1 108.00 1004.16
- A5 N1 A7 1 108.00 1004.16
- H C1 H 1 109.50 502.08
- H C2 H 1 109.50 502.08
- H C3 H 1 109.50 502.08
- H CP H 1 109.50 502.08
- O C1 H 1 109.00 502.08
- OH C1 H 1 109.00 502.08
- OH C2 H 1 109.00 502.08
- OH C3 H 1 109.00 502.08
- O2 C2 H 1 109.00 502.08
- OR C2 H 1 109.00 502.08
- O C1 C1 1 109.50 502.08
- O C1 C2 1 109.50 502.08
- O C1 C3 1 109.50 502.08
- OH C1 C1 1 107.90 502.08
- OH C1 C2 1 107.90 502.08
- OH C1 C3 1 107.90 502.08
- OH C2 C1 1 107.90 502.08
- OH C2 C2 1 107.90 502.08
- OH C2 C3 1 107.90 502.08
- O2 C2 C1 1 109.50 502.08
- O2 C2 C2 1 109.50 502.08
- O2 C2 C3 1 109.50 502.08
- OR C2 C1 1 109.50 502.08
- OR C2 C2 1 109.50 502.08
- OR C2 C3 1 109.50 502.08
- C1 C1 H 1 109.50 502.08
- C1 C2 H 1 109.50 502.08
- C1 C3 H 1 109.50 502.08
- C1 CP H 1 109.50 502.08
- C2 C1 H 1 109.50 502.08
- C2 C2 H 1 109.50 502.08
- C2 C3 H 1 109.50 502.08
- C3 C1 H 1 109.50 502.08
- C3 C2 H 1 109.50 502.08
- C3 C3 H 1 109.50 502.08
- CP C1 H 1 109.50 502.08
- CP CP H 1 109.50 502.08
- N C1 H 1 109.50 502.08
- N C2 H 1 109.50 502.08
- N C3 H 1 109.50 502.08
- N CP H 1 109.50 502.08
- N1 CP H 1 109.50 502.08
- N1 C1 H 1 109.50 502.08
- N1 C2 H 1 109.50 502.08
- N1 C3 H 1 109.50 502.08
- N2 CP H 1 109.50 502.08
- N2 C1 H 1 109.50 502.08
- N2 C2 H 1 109.50 502.08
- N2 C3 H 1 109.50 502.08
- M1 C1 H 1 109.50 502.08
- M1 C2 H 1 109.50 502.08
- M1 C3 H 1 109.50 502.08
- M2 C1 H 1 109.50 502.08
- M2 C2 H 1 109.50 502.08
- M2 C3 H 1 109.50 502.08
- M3 C1 H 1 109.50 502.08
- M3 C2 H 1 109.50 502.08
- M3 C3 H 1 109.50 502.08
- M1 C1 C1 1 111.00 502.08
- M1 C1 C2 1 111.00 502.08
- M1 C1 C3 1 111.00 502.08
- M1 C2 C1 1 111.00 502.08
- M1 C2 C2 1 111.00 502.08
- M1 C2 C3 1 111.00 502.08
- M2 C1 C1 1 111.00 502.08
- M2 C1 C2 1 111.00 502.08
- M2 C1 C3 1 111.00 502.08
- M2 C2 C1 1 111.00 502.08
- M2 C2 C2 1 111.00 502.08
- M2 C2 C3 1 111.00 502.08
- M3 C1 C1 1 111.00 502.08
- M3 C1 C2 1 111.00 502.08
- M3 C1 C3 1 111.00 502.08
- M3 C2 C1 1 111.00 502.08
- M3 C2 C2 1 111.00 502.08
- M3 C2 C3 1 111.00 502.08
- A6 C1 H 1 109.50 502.08
- A6 C2 H 1 109.50 502.08
- A6 C3 H 1 109.50 502.08
- A5 C1 H 1 109.50 502.08
- A5 C2 H 1 109.50 502.08
- A5 C3 H 1 109.50 502.08
- A7 C1 H 1 109.50 502.08
- A7 C2 H 1 109.50 502.08
- A7 C3 H 1 109.50 502.08
- Aprime C1 H 1 109.50 502.08
- Aprime C2 H 1 109.50 502.08
- Aprime C3 H 1 109.50 502.08
- Abis C2 H 1 109.50 502.08
- Abis C3 H 1 109.50 502.08
- Abis C1 H 1 109.50 502.08
- C1 C1 N 1 109.10 502.08
- C1 C1 N1 1 109.10 502.08
- C1 C1 N2 1 109.10 502.08
- C1 C2 N 1 109.10 502.08
- C1 C2 N1 1 109.10 502.08
- C1 C2 N2 1 109.10 502.08
- C2 C1 N 1 109.10 502.08
- C2 C1 N1 1 109.10 502.08
- C2 C1 N2 1 109.10 502.08
- C2 C2 N 1 109.10 502.08
- C2 C2 N1 1 109.10 502.08
- C2 C2 N2 1 109.10 502.08
- C3 C1 N 1 109.10 502.08
- C3 C1 N1 1 109.10 502.08
- C3 C1 N2 1 109.10 502.08
- C3 C2 N 1 109.10 502.08
- C3 C2 N1 1 109.10 502.08
- C3 C2 N2 1 109.10 502.08
- CP C1 N 1 104.00 502.08
- CP C1 N1 1 109.10 502.08
- CP C1 N2 1 109.10 502.08
- A6 C1 N 1 111.30 502.08
- A6 C1 N1 1 111.30 502.08
- A6 C1 N2 1 111.30 502.08
- A6 C2 N 1 111.30 502.08
- A6 C2 N1 1 111.30 502.08
- A6 C2 N2 1 111.30 502.08
- A5 C1 N 1 111.30 502.08
- A5 C1 N1 1 111.30 502.08
- A5 C1 N2 1 111.30 502.08
- A5 C2 N 1 111.30 502.08
- A5 C2 N1 1 111.30 502.08
- A5 C2 N2 1 111.30 502.08
- A7 C1 N 1 111.30 502.08
- A7 C1 N1 1 111.30 502.08
- A7 C1 N2 1 111.30 502.08
- A7 C2 N 1 111.30 502.08
- A7 C2 N1 1 111.30 502.08
- A7 C2 N2 1 111.30 502.08
- Aprime C1 N 1 111.30 502.08
- Aprime C1 N1 1 111.30 502.08
- Aprime C1 N2 1 111.30 502.08
- Aprime C2 N 1 111.30 502.08
- Aprime C2 N1 1 111.30 502.08
- Aprime C2 N2 1 111.30 502.08
- Abis C2 N 1 111.30 502.08
- Abis C2 N1 1 111.30 502.08
- Abis C2 N2 1 111.30 502.08
- A6 C1 M1 1 111.30 502.08
- A6 C1 M2 1 111.30 502.08
- A6 C1 M3 1 111.30 502.08
- A6 C2 M1 1 111.30 502.08
- A6 C2 M2 1 111.30 502.08
- A6 C2 M3 1 111.30 502.08
- A5 C1 M1 1 111.30 502.08
- A5 C1 M2 1 111.30 502.08
- A5 C1 M3 1 111.30 502.08
- A5 C2 M1 1 111.30 502.08
- A5 C2 M2 1 111.30 502.08
- A5 C2 M3 1 111.30 502.08
- A7 C1 M1 1 111.30 502.08
- A7 C1 M2 1 111.30 502.08
- A7 C1 M3 1 111.30 502.08
- A7 C2 M1 1 111.30 502.08
- A7 C2 M2 1 111.30 502.08
- A7 C2 M3 1 111.30 502.08
- Aprime C1 M1 1 111.30 502.08
- Aprime C1 M2 1 111.30 502.08
- Aprime C1 M3 1 111.30 502.08
- Aprime C2 M1 1 111.30 502.08
- Aprime C2 M2 1 111.30 502.08
- Aprime C2 M3 1 111.30 502.08
- Abis C2 M1 1 111.30 502.08
- Abis C2 M2 1 111.30 502.08
- Abis C2 M3 1 111.30 502.08
- Abis C1 M1 1 111.30 502.08
- Abis C1 M2 1 111.30 502.08
- Abis C1 M3 1 111.30 502.08
- Abis C1 N 1 111.30 502.08
- Abis C1 N1 1 111.30 502.08
- Abis C1 N2 1 111.30 502.08
- C1 C1 C1 1 111.40 502.08
- C1 C1 C2 1 111.40 502.08
- C1 C1 C3 1 111.40 502.08
- C1 C2 C1 1 111.40 502.08
- C1 C2 C2 1 111.40 502.08
- C1 C2 C3 1 111.40 502.08
- C1 CP CP 1 107.20 502.08
- C2 C1 C2 1 111.40 502.08
- C2 C1 C3 1 111.40 502.08
- C2 C2 C2 1 111.40 502.08
- C2 C2 C3 1 111.40 502.08
- C3 C1 C3 1 111.40 502.08
- C3 C2 C3 1 111.40 502.08
- CP CP CP 1 103.90 502.08
- N CP CP 1 105.10 502.08
- N1 CP CP 1 105.10 502.08
- N2 CP CP 1 105.10 502.08
- Aprime N CP 1 125.80 502.08
- A6 C1 C1 1 114.10 502.08
- A6 C1 C2 1 114.10 502.08
- A6 C1 C3 1 114.10 502.08
- A6 C2 C1 1 114.10 502.08
- A6 C2 C2 1 114.10 502.08
- A6 C2 C3 1 114.10 502.08
- A5 C1 C1 1 113.90 502.08
- A5 C1 C2 1 113.90 502.08
- A5 C1 C3 1 113.90 502.08
- A5 C2 C1 1 113.90 502.08
- A5 C2 C2 1 113.90 502.08
- A5 C2 C3 1 113.90 502.08
- A7 C1 C1 1 110.10 502.08
- A7 C1 C2 1 110.10 502.08
- A7 C1 C3 1 110.10 502.08
- A7 C2 C1 1 110.10 502.08
- A7 C2 C2 1 110.10 502.08
- A7 C2 C3 1 110.10 502.08
- Aprime C1 C1 1 110.10 502.08
- Aprime C1 C2 1 110.10 502.08
- Aprime C1 C3 1 110.10 502.08
- Aprime C1 CP 1 111.90 502.08
- Abis C1 CP 1 110.10 502.08
- Aprime C2 C1 1 110.10 502.08
- Aprime C2 C2 1 110.10 502.08
- Aprime C2 C3 1 110.10 502.08
- Abis C2 C1 1 110.10 502.08
- Abis C2 C2 1 110.10 502.08
- Abis C2 C3 1 110.10 502.08
- S C2 C1 1 115.50 502.08
- S C2 C2 1 115.50 502.08
- S C2 C3 1 115.50 502.08
- SH C2 C1 1 115.50 502.08
- SH C2 C2 1 115.50 502.08
- SH C2 C3 1 115.50 502.08
- S C2 H 1 110.00 502.08
- S C3 H 1 110.00 502.08
- SH C2 H 1 110.00 502.08
- C2 SH H 1 110.00 502.08
- H A6 H 1 120.00 502.08
- H A5 H 1 120.00 502.08
- H A7 H 1 120.00 502.08
- A6 A6 H 1 120.00 502.08
- A6 A7 H 1 120.00 502.08
- A5 A5 H 1 126.00 502.08
- A5 A7 H 1 120.00 502.08
- A7 A6 H 1 120.00 502.08
- A7 A5 H 1 126.00 502.08
- A7 A7 H 1 120.00 502.08
- O A6 O 1 120.00 502.08
- O Aprime O 1 120.00 502.08
- OH Aprime O 1 120.00 502.08
- O2 A6 O 1 120.00 502.08
- OR A6 O 1 120.00 502.08
- N A6 H 1 120.00 502.08
- N A5 H 1 126.00 502.08
- N A7 H 1 120.00 502.08
- N1 A6 H 1 120.00 502.08
- N1 A5 H 1 126.00 502.08
- N1 A7 H 1 120.00 502.08
- N2 A6 H 1 120.00 502.08
- N2 A5 H 1 126.00 502.08
- N2 A7 H 1 120.00 502.08
- N Aprime O 1 123.50 1004.16
- N1 Aprime O 1 123.50 1004.16
- N2 Aprime O 1 123.50 1004.16
- C1 Aprime O 1 121.00 502.08
- C1 Aprime OH 1 121.00 502.08
- C2 Aprime O 1 121.00 502.08
- C2 Aprime OH 1 121.00 502.08
- C3 Aprime O 1 121.00 502.08
- C3 Aprime C3 1 121.00 502.08
- C1 Aprime N 1 115.50 502.08
- C1 Aprime N1 1 115.50 502.08
- C1 Aprime N2 1 115.50 502.08
- C2 Aprime N 1 115.50 502.08
- C2 Aprime N1 1 115.50 502.08
- C2 Aprime N2 1 115.50 502.08
- C3 Aprime N 1 115.50 502.08
- C3 Aprime N1 1 115.50 502.08
- C3 Aprime N2 1 115.50 502.08
- Obis Abis C1 1 117.70 502.08
- Obis Abis C2 1 117.70 502.08
- Obis Abis C3 1 117.70 502.08
- Obis Abis Obis 1 124.60 1004.16
- C2 A5 A5 1 126.00 502.08
- C2 A5 L5 1 126.00 502.08
- L5 A5 H 1 126.00 502.08
- C2 A5 A7 1 126.00 502.08
- A5 A5 N 1 108.00 1004.16
- A5 A5 N1 1 108.00 1004.16
- A5 A5 N2 1 108.00 1004.16
- A5 A5 L5 1 108.00 1004.16
- N1 A5 L5 1 108.00 1004.16
- C2 A5 N1 1 126.00 502.08
- A7 A5 A5 1 108.00 1004.16
- M1 A6 M1 1 120.00 1004.16
- M1 A6 M2 1 120.00 1004.16
- M1 A6 M3 1 120.00 1004.16
- M2 A6 M2 1 120.00 1004.16
- M2 A6 M3 1 120.00 1004.16
- M3 A6 M3 1 120.00 1004.16
- A6 A6 C1 1 120.10 502.08
- A6 A6 C2 1 120.10 502.08
- A6 A6 C3 1 120.10 502.08
- A6 A6 A6 1 120.00 1004.16
- A6 A6 OH 1 118.40 502.08
- A7 A6 A6 1 120.00 1004.16
- A5 A7 A7 1 108.00 1004.16
- A7 A7 A6 1 120.00 1004.16
- A5 A7 A6 1 132.00 1004.16
- N A7 A6 1 132.00 502.08
- N1 A7 A6 1 132.00 502.08
- N2 A7 A6 1 132.00 502.08
- N1 A7 A7 1 108.00 1004.16
- L5 A7 A6 1 132.00 502.08
- L6 A7 A6 1 132.00 502.08
- C2 S C2 1 99.10 502.08
- C2 S C3 1 99.10 502.08
- S S C2 1 104.30 502.08
- HN M2 HN 1 120.00 502.08
- HN M3 HN 1 109.50 502.08
- C1 M1 HN 1 119.50 502.08
- C1 M2 HN 1 119.50 502.08
- C1 M3 HN 1 109.50 502.08
- C2 M1 HN 1 119.50 502.08
- C2 M2 HN 1 119.50 502.08
- C2 M3 HN 1 109.50 502.08
- C3 M1 HN 1 119.50 502.08
- C3 M2 HN 1 119.50 502.08
- C3 M3 HN 1 109.50 502.08
- A6 M1 HN 1 119.60 502.08
- A6 M2 HN 1 119.60 502.08
- A6 M3 HN 1 119.60 502.08
- A6 M1 C1 1 123.20 502.08
- A6 M1 C2 1 123.20 502.08
- A6 M1 C3 1 123.20 502.08
- A6 M2 C1 1 123.20 502.08
- A6 M2 C2 1 123.20 502.08
- A6 M2 C3 1 123.20 502.08
- A6 M3 C1 1 123.20 502.08
- A6 M3 C2 1 123.20 502.08
- A6 M3 C3 1 123.20 502.08
- A5 L5 A5 1 108.00 1004.16
- A6 N1 A6 1 120.00 502.08
- OH C1 N 1 109.50 502.08
- OH C1 N1 1 109.50 502.08
- OH C1 N2 1 109.50 502.08
- C3 A7 A6 1 108.86 502.08
- C3 A7 A7 1 132.53 502.08
- L5 A7 A7 1 108.00 502.08
- A7 A7 L6 1 120.00 502.08
- A5 L5 A7 1 108.00 502.08
- A6 L5 A7 1 119.33 502.08
- N1 A5 N1 1 108.00 1004.16
- Y A6 H 1 120.00 502.08
- Z C2 H 1 110.00 502.08
- Z C3 H 1 110.00 502.08
- Z A6 H 1 120.00 502.08
- A6 N FE 1 120.00 502.08
- A6 N1 FE 1 120.00 502.08
- A6 N2 FE 1 120.00 502.08
- A5 N FE 1 120.00 502.08
- A5 N1 FE 1 120.00 502.08
- A5 N2 FE 1 120.00 502.08
- A7 N FE 1 120.00 502.08
- A7 N1 FE 1 120.00 502.08
- A7 N2 FE 1 120.00 502.08
- Aprime N FE 1 120.00 502.08
- Aprime N1 FE 1 120.00 502.08
- Aprime N2 FE 1 120.00 502.08
- Y R Y 1 105.40 1004.16
- Y A6 Y 1 124.50 502.08
- Y Aprime Y 1 124.50 502.08
- Y W Y 1 105.40 502.08
- FE W Y 1 127.30 502.08
- R Y A6 1 125.50 1004.16
- R Y Aprime 1 125.50 1004.16
- W Y A6 1 125.20 1004.16
- W Y Aprime 1 125.20 1004.16
- Z Y A6 1 124.20 1004.16
- Z Y Aprime 1 124.20 1004.16
- Z Y R 1 109.50 1004.16
- Z Y W 1 109.50 1004.16
- Y Z C2 1 125.40 502.08
- Y Z C3 1 125.40 502.08
- Y Z A6 1 124.40 1004.16
- Y Z Aprime 1 124.40 1004.16
- Z Z C2 1 127.50 502.08
- Z Z C3 1 127.50 502.08
- Z Z A6 1 128.40 1004.16
- Z Z Aprime 1 128.40 1004.16
- Z Z Y 1 107.00 1004.16
- Z C2 C1 1 109.50 502.08
- Z C2 C2 1 109.50 502.08
- Z C2 C3 1 109.50 502.08
- Z A6 A6 1 120.00 1004.16
- Z A6 A7 1 120.00 1004.16
- W FE N 1 90.00 502.08
- W FE N1 1 90.00 502.08
- W FE N2 1 90.00 502.08
- W FE W 1 180.00 502.08
- OF FE N 1 180.00 502.08
- OF FE N1 1 180.00 502.08
- OF FE N2 1 180.00 502.08
- OF FE W 1 90.00 502.08
- OF OF FE 1 120.00 502.08
-
-
-[ dihedraltypes ]
-; Encad proper dihedrals. Note that there is a difference pf
-; sign in the cosine definition between Gromacs and Encad. All angle values
-; here are thus offset 180 degrees.
- ; i l func q0 cq
- C1 A6 A6 H 1 180.00 167.36 1
- C2 A6 A6 H 1 180.00 167.36 1
- C2 A5 A5 H 1 180.00 167.36 1
- C2 A5 A7 H 1 180.00 167.36 1
- C3 A6 A6 H 1 180.00 167.36 1
- C3 A7 A6 H 1 180.00 167.36 1
- C3 A7 A7 H 1 180.00 167.36 1
- C2 A5 A7 A6 1 180.00 167.36 1
- H A6 N C1 1 180.00 167.36 1
- A6 A6 A6 H 1 0.00 167.36 1
- L5 A7 A7 L5 1 0.00 167.36 1
- L5 A7 A7 L6 1 0.00 167.36 1
- L6 A7 A7 L6 1 0.00 167.36 1
- N A7 A6 A6 1 0.00 167.36 1
- N1 A7 A6 A6 1 0.00 167.36 1
- N2 A7 A6 A6 1 0.00 167.36 1
- N1 A7 A7 A6 1 0.00 167.36 1
- A6 A7 L5 A5 1 180.00 83.68 2
- A7 A7 N1 A5 1 180.00 167.36 1
- Aprime N C1 Aprime 1 0.00 0.00 0 ; will be removed by grompp
- Aprime N C2 Aprime 1 0.00 0.00 0 ; will be removed by grompp
- Aprime N1 C1 Aprime 1 0.00 0.00 0 ; will be removed by grompp
- Aprime N1 C2 Aprime 1 0.00 0.00 0 ; will be removed by grompp
- Aprime N2 C1 Aprime 1 0.00 0.00 0 ; will be removed by grompp
- Aprime N2 C2 Aprime 1 0.00 0.00 0 ; will be removed by grompp
- HN N2 Aprime N2 1 180.00 41.84 2 ; not present in aanahn
- C1 Aprime N C1 1 180.00 41.84 2
- C1 Aprime N C2 1 180.00 41.84 2
- C1 Aprime N C3 1 180.00 41.84 2
- C1 Aprime N1 C1 1 180.00 41.84 2
- C1 Aprime N1 C2 1 180.00 41.84 2
- C1 Aprime N1 C3 1 180.00 41.84 2
- C1 Aprime N2 C1 1 180.00 41.84 2
- C1 Aprime N2 C2 1 180.00 41.84 2
- C1 Aprime N2 C3 1 180.00 41.84 2
- C2 Aprime N C1 1 180.00 41.84 2
- C2 Aprime N C2 1 180.00 41.84 2
- C2 Aprime N C3 1 180.00 41.84 2
- C2 Aprime N1 C1 1 180.00 41.84 2
- C2 Aprime N1 C2 1 180.00 41.84 2
- C2 Aprime N1 C3 1 180.00 41.84 2
- C2 Aprime N2 C1 1 180.00 41.84 2
- C2 Aprime N2 C2 1 180.00 41.84 2
- C2 Aprime N2 C3 1 180.00 41.84 2
- C3 Aprime N C1 1 180.00 41.84 2
- C3 Aprime N C2 1 180.00 41.84 2
- C3 Aprime N C3 1 180.00 41.84 2
- C3 Aprime N1 C1 1 180.00 41.84 2
- C3 Aprime N1 C2 1 180.00 41.84 2
- C3 Aprime N1 C3 1 180.00 41.84 2
- C3 Aprime N2 C1 1 180.00 41.84 2
- C3 Aprime N2 C2 1 180.00 41.84 2
- C3 Aprime N2 C3 1 180.00 41.84 2
- C1 Aprime N1 HN 1 180.00 41.84 2
- C1 Aprime N2 HN 1 180.00 41.84 2
- C2 Aprime N1 HN 1 180.00 41.84 2
- C2 Aprime N2 HN 1 180.00 41.84 2
- C3 Aprime N1 HN 1 180.00 41.84 2
- C3 Aprime N2 HN 1 180.00 41.84 2
- C1 A6 A6 A6 1 0.00 334.72 1
- C2 A6 A6 A6 1 0.00 334.72 1
- C3 A6 A6 A6 1 0.00 334.72 1
- A6 A6 A6 A6 1 180.00 334.72 1
- N C1 CP CP 1 180.00 41.84 1
- N1 C1 CP CP 1 180.00 41.84 1
- N2 C1 CP CP 1 180.00 41.84 1
- C1 Aprime N CP 1 180.00 41.84 2
- C2 Aprime N CP 1 180.00 41.84 2
- C3 Aprime N CP 1 180.00 41.84 2
- Aprime N CP CP 1 0.00 41.84 1
- C1 A6 A6 X 1 180.00 41.84 2
- C2 A6 A6 X 1 180.00 41.84 2
- C2 A5 A5 X 1 180.00 41.84 2
- C2 A5 A7 X 1 180.00 41.84 2
- C3 A6 A6 X 1 180.00 41.84 2
- C3 A7 A6 X 1 180.00 41.84 2
- C3 A7 A7 X 1 180.00 41.84 2
- X A5 N C1 1 0.00 167.36 1
- X A5 N C2 1 0.00 167.36 1
- X A5 N C3 1 0.00 167.36 1
- X A5 N1 C1 1 0.00 167.36 1
- X A5 N1 C2 1 0.00 167.36 1
- X A5 N1 C3 1 0.00 167.36 1
- X A5 N2 C1 1 0.00 167.36 1
- X A5 N2 C2 1 0.00 167.36 1
- X A5 N2 C3 1 0.00 167.36 1
- C2 A5 N1 X 1 0.00 167.36 1
- X A6 N C1 1 0.00 167.36 1
- X A6 N C2 1 0.00 167.36 1
- X A6 N C3 1 0.00 167.36 1
- X A7 N C1 1 180.00 167.36 1
- X A7 N C2 1 180.00 167.36 1
- X A7 N C3 1 180.00 167.36 1
- X A7 N1 C1 1 180.00 167.36 1
- X A7 N1 C2 1 180.00 167.36 1
- X A7 N1 C3 1 180.00 167.36 1
- X A7 N2 C1 1 180.00 167.36 1
- X A7 N2 C2 1 180.00 167.36 1
- X A7 N2 C3 1 180.00 167.36 1
- S S C2 X 1 0.00 0.00 0 ; will be removed by grompp
- X A6 A6 X 1 180.00 167.36 1
- X A6 A7 X 1 180.00 167.36 1
- X A5 A5 X 1 180.00 167.36 1
- X A5 A7 X 1 180.00 167.36 1
- X A7 A7 X 1 180.00 167.36 1
- X A5 N X 1 180.00 334.72 2
- X A5 N1 X 1 180.00 334.72 2
- X A5 N2 X 1 180.00 334.72 2
- X A5 L5 X 1 180.00 41.84 2
- X A6 N X 1 180.00 167.36 1
- X A6 N1 X 1 180.00 167.36 1
- X A6 N2 X 1 180.00 167.36 1
- X A6 L5 X 1 180.00 167.36 1
- X A6 L6 X 1 180.00 167.36 1
- X A7 L5 X 1 180.00 167.36 1
- X A7 L6 X 1 180.00 167.36 1
- X P O2 X 1 0.00 8.368 3
- X P OP X 1 0.00 8.368 3
- X N C1 X 1 0.00 0.00 0 ; will be removed by grompp
- X N C2 X 1 0.00 0.00 0 ; will be removed by grompp
- X N C3 X 1 0.00 0.00 0 ; will be removed by grompp
- X N CP X 1 0.00 0.00 0 ; will be removed by grompp
- X N1 C1 X 1 0.00 0.00 0 ; will be removed by grompp
- X N1 C2 X 1 0.00 0.00 0 ; will be removed by grompp
- X N1 C3 X 1 0.00 0.00 0 ; will be removed by grompp
- X N1 CP X 1 0.00 0.00 0 ; will be removed by grompp
- X N2 C1 X 1 0.00 0.00 0 ; will be removed by grompp
- X N2 C2 X 1 0.00 0.00 0 ; will be removed by grompp
- X N2 C3 X 1 0.00 0.00 0 ; will be removed by grompp
- X N2 CP X 1 0.00 0.00 0 ; will be removed by grompp
- X C1 O X 1 0.00 2.5104 3
- X C1 OH X 1 0.00 2.5104 3
- X C2 OH X 1 0.00 2.5104 3
- X C2 O2 X 1 0.00 2.5104 3
- X C2 OR X 1 0.00 2.5104 3
- X C3 OH X 1 0.00 2.5104 3
- X C1 C1 X 1 0.00 5.8576 3
- X C1 C2 X 1 0.00 5.8576 3
- X C1 C3 X 1 0.00 5.8576 3
- X C2 C2 X 1 0.00 5.8576 3
- X C2 C3 X 1 0.00 5.8576 3
- X C3 C3 X 1 0.00 5.8576 3
- X C1 CP X 1 180.00 5.8576 3
- X CP CP X 1 180.00 5.8576 3
- X C1 Aprime X 1 0.00 0.00 0 ; will be removed by grompp
- X C2 Aprime X 1 0.00 0.00 0 ; will be removed by grompp
- X C3 Aprime X 1 0.00 0.00 0 ; will be removed by grompp
- X CP Aprime X 1 0.00 0.00 0 ; will be removed by grompp
- X C1 A6 X 1 0.00 0.4184 6
- X C1 A5 X 1 0.00 0.4184 6
- X C1 A7 X 1 0.00 0.4184 6
- X C1 Abis X 1 0.00 0.4184 6
- X C2 A6 X 1 0.00 0.4184 6
- X C2 A5 X 1 0.00 0.4184 6
- X C2 A7 X 1 0.00 0.4184 6
- X C2 Abis X 1 0.00 0.4184 6
- X C3 A6 X 1 0.00 0.4184 6
- X C3 A5 X 1 0.00 0.4184 6
- X C3 A7 X 1 0.00 0.4184 6
- X C3 Abis X 1 0.00 0.4184 6
- X C1 M3 X 1 0.00 5.8576 3
- X C2 M3 X 1 0.00 5.8576 3
- X C3 M3 X 1 0.00 5.8576 3
- X A6 O2 X 1 0.00 2.5104 3
- X Aprime OH X 1 0.00 2.5104 3
- X A6 OH X 1 0.00 2.5104 3
- X A6 M1 X 1 180.00 41.84 2
- X A6 M2 X 1 180.00 41.84 2
- X A6 M3 X 1 180.00 41.84 2
- X S C2 X 1 0.00 4.184 3
- X S C3 X 1 0.00 4.184 3
- X SH C2 X 1 0.00 4.184 3
- X S S X 1 0.00 25.104 2
- X M1 C1 X 1 0.00 5.8576 3
- X M1 C2 X 1 0.00 5.8576 3
- X M1 C3 X 1 0.00 5.8576 3
- X M2 C1 X 1 0.00 5.8576 3
- X M2 C2 X 1 0.00 5.8576 3
- X M2 C3 X 1 0.00 5.8576 3
- X Y A6 X 1 180.00 41.84 2
- X Y Aprime X 1 180.00 41.84 2
- X Y R X 1 180.00 83.68 2
- X Y W X 1 180.00 83.68 2
- X Z C2 X 1 0.00 0.4184 6
- X Z C3 X 1 0.00 0.4184 6
- X Z A6 X 1 180.00 41.84 2
- X Z Aprime X 1 180.00 41.84 2
- X Z Y X 1 180.00 83.68 2
- X Z Z X 1 180.00 83.68 2
- X FE N X 1 0.00 0.00 0 ; will be removed by grompp
- X FE N1 X 1 0.00 0.00 0 ; will be removed by grompp
- X FE N2 X 1 0.00 0.00 0 ; will be removed by grompp
- X FE W X 1 0.00 0.00 0 ; will be removed by grompp
- X OF FE X 1 0.00 0.00 0 ; will be removed by grompp
-
-
-
-; Encad out-of-plane potentials are the same functional form as
-; Gromacs proper dihedrals (i.e. cosine, but with shifted sign).
-; Note that the atom order is different too; In Gromacs, the first atom
-; of an improper is the center one, while it is the 3rd in Encad.
-
-; Since they use the same type as proper dihedrals we use defines here
-; to avoid mistakes in ambiguous cases.
-;
-; Note: the three parameters are repeated, to avoid having the free energy B state
-; picked up from the default proper dihedral parameter types
-; (grompp would give errors about non-matching multiplicity between A/B states)
-;
-; DNA
-#define improper_X_X_P_X 180.0 8.368 3 180.0 8.368 3
-#define improper_X_X_M2_X 180.0 8.368 2 180.0 8.368 2
-; Proteins
-#define improper_X_X_N_X 180.0 8.368 2 180.0 8.368 2
-#define improper_X_X_C_X 180.0 8.368 3 180.0 8.368 3
-#define improper_X_X_A_X 180.0 8.368 2 180.0 8.368 2
-#define improper_A_X_C1_X 60.0 75.312 1 60.0 75.312 1
-#define improper_A_X_C1_H -60.0 75.312 1 -60.0 75.312 1
-#define improper_X_X_C1_A 60.0 75.312 1 60.0 75.312 1
-#define improper_C3_C2_C1_C3 60.0 75.312 1 60.0 75.312 1
-#define improper_C_C1_C1_C3 60.0 75.312 1 60.0 75.312 1
-#define improper_C3_C1_C1_OH -60.0 75.312 1 -60.0 75.312 1
-#define improper_C1_C2_C1_C3 -60.0 75.312 1 -60.0 75.312 1
-#define improper_N_A_C1_C -60.0 75.312 1 -60.0 75.312 1
-#define improper_M_A_C1_C -60.0 75.312 1 -60.0 75.312 1
-#define improper_X_X_M_X 180.0 8.368 2 180.0 8.368 2
-#define improper_X_X_M3_X 180.0 8.368 3 180.0 8.368 3
-; Heme
-#define improper_X_X_R_X 180.0 8.368 2 180.0 8.368 2
-#define improper_X_X_W_X 180.0 8.368 2 180.0 8.368 2
-#define improper_X_X_Y_X 180.0 8.368 2 180.0 8.368 2
-#define improper_X_X_Z_X 180.0 8.368 2 180.0 8.368 2
-#define improper_X_X_FE_X 180.0 0.000 4 180.0 0.000 4
-#define improper_X_X_OF_X 180.0 8.368 2 180.0 8.368 2
-
-
-
+++ /dev/null
-[ atomtypes ]
-;name at.num mass charge ptype sigma epsilon
- H 1 1.008 0.0 A 2.54129e-01 1.58992e-01
- O 8 15.9994 0.0 A 2.76223e-01 7.73161e-01
- N 7 14.0027 0.0 A 3.40065e-01 1.72862e+00
- N1 7 14.0027 0.0 A 3.40065e-01 1.72862e+00
- N2 7 14.0027 0.0 A 3.40065e-01 1.72862e+00
- C1 6 12.011 0.0 A 3.84423e-01 3.08863e-01
- C2 6 12.011 0.0 A 3.84423e-01 3.08863e-01
- C3 6 12.011 0.0 A 3.84423e-01 3.08863e-01
- CP 6 12.011 0.0 A 3.84423e-01 3.08863e-01
- A6 6 12.011 0.0 A 3.75977e-01 1.57444e-01
- A5 6 12.011 0.0 A 3.75977e-01 1.57444e-01
- A7 6 12.011 0.0 A 3.75977e-01 1.57444e-01
- Aprime 6 12.011 0.0 A 3.75977e-01 1.57444e-01
- Abis 6 12.011 0.0 A 3.75977e-01 1.57444e-01
- L5 7 14.0027 0.0 A 2.76223e-01 7.73161e-01
- L6 7 14.0027 0.0 A 2.76223e-01 7.73161e-01
- P 15 30.9738 0.0 A 3.84423e-01 3.08863e-01
- OH 8 15.9994 0.0 A 3.16556e-01 7.73161e-01
- O2 8 15.9994 0.0 A 3.16556e-01 7.73161e-01
- OR 8 15.9994 0.0 A 3.16556e-01 7.73161e-01
- S 16 32.060 0.0 A 3.84423e-01 3.08863e-01
- SH 16 32.060 0.0 A 3.84423e-01 3.08863e-01
- M1 7 14.0027 0.0 A 3.40065e-01 1.72862e+00
- M2 7 14.0027 0.0 A 3.40065e-01 1.72862e+00
- M3 7 14.0027 0.0 A 3.40065e-01 1.72862e+00
- HN 1 1.008 0.0 A 4.45449e-02 4.18400e-02
- HO 1 1.008 0.0 A 4.45449e-02 4.18400e-02
- HW 1 1.008 0.0 A 4.45449e-02 4.18400e-02
- CL 17 35.453 0.0 A 4.31068e-01 3.51456e-01
- Obis 8 15.9994 0.0 A 2.76223e-01 7.73161e-01
- OP 8 15.9994 0.0 A 2.76223e-01 7.73161e-01
- R 7 14.0027 0.0 A 3.40065e-01 1.72862e+00
- W 7 14.0027 0.0 A 3.40065e-01 1.72862e+00
- Y 6 12.011 0.0 A 3.75977e-01 1.57444e-01
- Z 6 12.011 0.0 A 3.75977e-01 1.57444e-01
- FE 26 55.847 0.0 A 3.84423e-01 3.08863e-01
- OF 8 15.9994 0.0 A 2.76223e-01 7.73161e-01
- OW 8 15.9994 0.0 A 3.16556e-01 7.73161e-01
- AR 18 39.948 0.0 A 2.54129e-01 1.58992e-01
- NA 11 22.9898 0.0 A 2.40543e-01 7.73161e-01
- MCH3 0 0.0 0.0 A 0.0 0.0
- MNH3 0 0.0 0.0 A 0.0 0.0
- MW 0 0.0 0.0 D 0.0 0.0
-
-[ nonbond_params ]
- ; i j func c6 c12
-; Encad uses strict combination rules, so no need for explicit parameters
-
-[ pairtypes ]
- ; i j func cs6 cs12
-; 1,4 interactions are calculated automatically, using fudge factors.
-; (In the current version, the factors are 0.0, meaning no 1,4 interactions).
-
+++ /dev/null
-[DEPRECATED] Encad all-atom force field, using full solvent charges
+++ /dev/null
-#define _FF_ENCAD
-; Implemented from encad library version 25/xi/91,
-; with 1,4 interaction setup modified by Michael Levitt.
-; In this forcefield, both coulombic and Lennard-Jones interactions
-; are completely excluded for 1,4 interaction sites.
-;
-; Vacuum version - scaled down charges.
-
-;
-[ defaults ]
-; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
- 1 3 yes 0.0 0.0
-
-#include "ffnonbonded.itp"
-#include "ffbonded.itp"
-
-
-
-
+++ /dev/null
-f3c F3C flexible three-centered water model
+++ /dev/null
-[ None ]
-
-[ COO- ]
-[ replace ]
-C C Abis 12.011 0.64
-O O1 Obis 15.9994 -0.42
-OXT O2 Obis 15.9994 -0.42
-[ add ]
-2 8 O C CA N
- Obis 15.9994 -0.92
-[ dihedrals ]
-N CA C O2
-[ impropers ]
-CA O2 C O1 improper_X_X_A_X
-N C CA CB improper_X_X_C_X
-
-[ COOH ]
-[ replace ]
-C C Aprime 12.011 0.38
-O O OH 15.9994 -0.38
-OXT OT O 15.9994 -0.433
-[ add ]
-1 2 OT C CA N
- O 15.9994 -0.433
-1 2 HO O C CA
- HO 1.008 0.433
-[ dihedrals ]
-N CA C O
-[ impropers ]
-OT CA C O improper_X_X_A_X
-
+++ /dev/null
-ACE 1
-3 4 HH3 CH3 C O
-ALA 3
-1 1 H N -C CA
-1 5 HA CA N C CB
-3 4 HB CB CA N
-ARG 8
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-2 6 HG CG CD CB
-2 6 HD CD NE CG
-1 1 HE NE CD CZ
-2 3 HH1 NH1 CZ NE
-2 3 HH2 NH2 CZ NE
-ARGN 8
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-2 6 HG CG CD CB
-2 6 HD CD NE CG
-1 1 HE NE CD CZ
-1 2 HH1 NH1 CZ NE
-2 3 HH2 NH2 CZ NE
-ASN 4
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-2 3 HD2 ND2 CG CB
-ASP 3
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-ASPH 4
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-1 2 HD2 OD2 CG CB
-CYS2 3
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB SG CA
-CYSH 4
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB SG CA
-1 2 HG SG CB CA
-GLN 5
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-2 6 HG CG CD CB
-2 3 HE2 NE2 CD CG
-GLU 4
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-2 6 HG CG CD CB
-GLUH 5
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-2 6 HG CG CD CB
-1 2 HE2 OE2 CD CG
-GLY 2
-1 1 H N -C CA
-2 6 HA CA C N
-HIS1 6
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-1 1 HD2 CD2 CG NE2
-1 1 HE1 CE1 ND1 NE2
-1 1 HD1 ND1 CG CE1
-HISA 6
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-1 1 HD2 CD2 CG NE2
-1 1 HE1 CE1 ND1 NE2
-1 1 HD1 ND1 CG CE1
-HISB 6
-1 1 H N -C CA
-2 6 HB CB CG CA
-1 5 HA CA N C CB
-1 1 HE2 NE2 CE1 CD2
-1 1 HD2 CD2 CG NE2
-1 1 HE1 CE1 ND1 NE2
-HISH 7
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-1 1 HD2 CD2 CG NE2
-1 1 HE1 CE1 ND1 NE2
-1 1 HD1 ND1 CG CE1
-1 1 HE2 NE2 CE1 CD2
-HOH 1
-2 7 HW OW
-ILE 6
-1 1 H N -C CA
-1 5 HA CA N C CB
-1 5 HB CB CA CG1 CG2
-2 6 HG1 CG1 CD CB
-3 4 HG2 CG2 CB CA
-3 4 HD CD CG1 CB
-LEU 6
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-1 5 HG CG CB CD1 CD2
-3 4 HD1 CD1 CG CB
-3 4 HD2 CD2 CG CB
-LYS 7
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-2 6 HG CG CD CB
-2 6 HD CD CE CG
-2 6 HE CE NZ CD
-2 4 HZ NZ CE CD
-LYSH 7
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-2 6 HG CG CD CB
-2 6 HD CD CE CG
-2 6 HE CE NZ CD
-3 4 HZ NZ CE CD
-MET 5
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-2 6 HG CG SD CB
-3 4 HE CE SD CG
-NAC 2
-1 1 H N -C CA
-3 4 HA CA N -C
-NH2 1
-2 3 H N -C -CA
-PHE 8
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-1 1 HD1 CD1 CG CE1
-1 1 HD2 CD2 CG CE2
-1 1 HE1 CE1 CD1 CZ
-1 1 HE2 CE2 CD2 CZ
-1 1 HZ CZ CE1 CE2
-PRO 4
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-2 6 HG CG CD CB
-2 6 HD CD N CG
-SER 4
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB OG CA
-1 2 HG OG CB CA
-THR 5
-1 1 H N -C CA
-1 5 HA CA N C CB
-1 5 HB CB CA OG1 CG2
-1 2 HG1 OG1 CB CA
-3 4 HG2 CG2 CB CA
-TRP 9
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-1 1 HD1 CD1 NE1 CG
-1 1 HE1 NE1 CD1 CE2
-1 1 HE3 CE3 CD2 CZ3
-1 1 HZ3 CZ3 CE3 CH2
-1 1 HH2 CH2 CZ3 CZ2
-1 1 HZ2 CZ2 CE2 CH2
-TYR 8
-1 1 H N -C CA
-1 5 HA CA N C CB
-2 6 HB CB CG CA
-1 1 HD1 CD1 CG CE1
-1 1 HD2 CD2 CG CE2
-1 1 HE1 CE1 CD1 CZ
-1 1 HE2 CE2 CD2 CZ
-1 2 HH OH CZ CE1
-VAL 5
-1 1 H N -C CA
-1 5 HA CA N C CB
-1 5 HB CB CA CG1 CG2
-3 4 HG1 CG1 CB CA
-3 4 HG2 CG2 CB CA
+++ /dev/null
-[ None ]
-
-[ NH3+ ]
-[ replace ]
-N M3 14.0067 -0.91
-[ add ]
-3 4 H N CA C
- HN 1.008 0.37
-[ delete ]
-H
-[ dihedrals ]
-H1 N CA C
-[ impropers ]
-H1 CA N H2 improper_X_X_M3_X
-H1 CA N H3 improper_X_X_M3_X
-
-[ NH2 ]
-[ replace ]
-N N2 14.0067 -0.666
-[ add ]
-2 4 H N CA C
- HN 1.008 0.333
-[ delete ]
-H
-[ dihedrals ]
-H1 N CA C
-[ impropers ]
-H1 CA N H2 improper_X_X_M_X
-
-[ PRO-NH2+ ]
-[ replace ]
-N N2 14.0067 -0.666
-[ add ]
-2 4 H N CA C
- HN 1.008 0.333
-[ dihedrals ]
-H1 N CA C
-[ impropers ]
-H1 CA N H2 improper_X_X_M_X
-
-[ PRO-NH ]
-[ replace ]
-N N1 14.0067 -0.333
-[ add ]
-1 4 H N CA C
- HN 1.008 0.333
-[ dihedrals ]
-H1 N CA C
-
+++ /dev/null
-; rtp residue to rtp building block table
-;GMX Force-field
-CYS CYSH
-HISD HISA
-HISE HISB
-LYS LYSH
-LYSN LYS
+++ /dev/null
-;
-; 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 ]
-; Column 1 : default bondtype
-; Column 2 : default angletype
-; Column 3 : default proper dihedraltype
-; Column 4 : default improper dihedraltype
-; Column 5 : This controls the generation of dihedrals from the bonding.
-; All possible dihedrals are generated automatically. A value of
-; 1 here means that all these are retained. A value of
-; 0 here requires generated dihedrals be removed if
-; * there are any dihedrals on the same central atoms
-; specified in the residue topology, or
-; * there are other identical generated dihedrals
-; sharing the same central atoms, or
-; * there are other generated dihedrals sharing the
-; same central bond that have fewer hydrogen atoms
-; Column 6 : number of neighbors to exclude from non-bonded interactions
-; Column 7 : 1 = generate 1,4 interactions between pairs of hydrogen atoms
-; 0 = do not generate such
-; Column 8 : 1 = remove proper dihedrals if found centered on the same
-; bond as an improper dihedral
-; 0 = do not generate such
-; bonds angles dihedrals impropers all_dihedrals nrexcl bHH14 bRemoveDih
- 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 0.333 5
- CZ A6 0.000 6
- NH1 M2 -0.666 7
- HH11 HN 0.383 7
- HH12 HN 0.383 7
- NH2 M2 -0.666 8
- HH21 HN 0.383 8
- HH22 HN 0.383 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 0.383 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 0.640 3
- OD1 Obis -0.420 3
- OD2 Obis -0.420 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 0.640 4
- OE1 Obis -0.420 4
- OE2 Obis -0.420 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 0.000 3
- ND1 N1 -0.300 4
- HD1 HN 0.375 4
- CE1 A5 -0.119 6
- HE1 H 0.119 6
- NE2 N1 -0.300 7
- HE2 HN 0.375 7
- CD2 A5 -0.119 5
- HD2 H 0.119 5
- C Aprime 0.380 8
- O O -0.380 8
- [ 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
-
-
-[ HIP ] ; same as HISH
- [ 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 0.000 3
- ND1 N1 -0.300 4
- HD1 HN 0.375 4
- CE1 A5 -0.119 6
- HE1 H 0.119 6
- NE2 N1 -0.300 7
- HE2 HN 0.375 7
- CD2 A5 -0.119 5
- HD2 H 0.119 5
- C Aprime 0.380 8
- O O -0.380 8
- [ 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 -0.910 6
- HZ1 HN 0.370 6
- HZ2 HN 0.370 6
- HZ3 HN 0.370 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
-
+++ /dev/null
- H 1.008 ; Hydrogen bound to carbon
- O 15.9994 ; Oxygen
- N 14.0067 ; Trivalent nitrogen
- N1 14.0067 ; Trivalent nitrogen
- N2 14.0067 ; Trivalent nitrogen
- C1 12.011 ; Aliphatic carbon
- C2 12.011 ; Aliphatic carbon
- C3 12.011 ; Aliphatic carbon
- CP 12.011 ; Aliphatic carbon
- A6 12.011 ; Aromatic carbon
- A5 12.011 ; Aromatic carbon
- A7 12.011 ; Aromatic carbon
- Aprime 12.011 ; Aromatic carbon
- Abis 12.011 ; Aromatic carbon
- L5 14.0067 ; Acceptor nitrogen
- L6 14.0067 ; Acceptor nitrogen
- P 30.9738 ; Phosphorus
- OH 15.9994 ; Divalent oxygen
- O2 15.9994 ; Divalent oxygen
- OR 15.9994 ; Divalent oxygen
- S 32.060 ; Sulphur not bound to hydrogen
- SH 32.060 ; Sulphur with bound hydrogen
- M1 14.0067 ; Charged nitrogen
- M2 14.0067 ; Charged nitrogen
- M3 14.0067 ; Charged nitrogen
- HN 1.008 ; Polar hydrogen
- HO 1.008 ; Polar hydrogen
- HW 1.008 ; Water hydrogen
- CL 35.453 ; Chloride ion
- Obis 15.9994 ; Charged oxygen
- OP 15.9994 ; Charged oxygen
- R 14.0067 ; Heme nitrogen
- W 14.0067 ; Heme nitrogen
- Y 12.011 ; Heme carbon
- Z 12.011 ; Heme carbon
- FE 55.847 ; Heme Iron
- OF 15.9994 ; Heme oxygen
- OW 15.9994 ; Water oxygen
- AR 39.948 ; Argon
- NA 22.9898 ; Sodium
- MCH3 0 ; Dummy
- MNH3 0 ; Dummy
- MW 0 ; Dummy
+++ /dev/null
-[ bondtypes ]
- ; i j func b0 kb
- OW HW 1 0.10000 209200.0
- OH HO 1 0.10000 209200.0
- N1 HN 1 0.10000 209200.0
- N2 HN 1 0.10000 209200.0
- C1 H 1 0.10900 209200.0
- C2 H 1 0.10900 209200.0
- C3 H 1 0.10900 209200.0
- CP H 1 0.10900 209200.0
- C1 O 1 0.14370 209200.0
- C2 O2 1 0.14370 209200.0
- C2 OR 1 0.14370 209200.0
- C1 OH 1 0.14390 209200.0
- C2 OH 1 0.14390 209200.0
- C3 OH 1 0.14390 209200.0
- C1 N 1 0.14670 209200.0
- C1 N1 1 0.14670 209200.0
- C1 N2 1 0.14670 209200.0
- C2 N 1 0.14670 209200.0
- C2 N1 1 0.14670 209200.0
- C2 N2 1 0.14670 209200.0
- C3 N 1 0.14670 209200.0
- C3 N1 1 0.14670 209200.0
- C3 N2 1 0.14670 209200.0
- CP N 1 0.14670 209200.0
- CP N1 1 0.14670 209200.0
- CP N2 1 0.14670 209200.0
- C1 M1 1 0.14720 209200.0
- C1 M2 1 0.14720 209200.0
- C1 M3 1 0.14720 209200.0
- C2 M1 1 0.14720 209200.0
- C2 M2 1 0.14720 209200.0
- C2 M3 1 0.14720 209200.0
- C3 M1 1 0.14720 209200.0
- C3 M2 1 0.14720 209200.0
- C3 M3 1 0.14720 209200.0
- C1 C1 1 0.15250 209200.0
- C1 C2 1 0.15250 209200.0
- C1 C3 1 0.15250 209200.0
- C2 C2 1 0.15250 209200.0
- C2 C3 1 0.15250 209200.0
- C3 C3 1 0.15250 209200.0
- CP CP 1 0.15190 209200.0
- C1 CP 1 0.14980 209200.0
- A6 H 1 0.10900 209200.0
- A5 H 1 0.10900 209200.0
- A7 H 1 0.10900 209200.0
- A6 C1 1 0.15260 209200.0
- A6 C2 1 0.15260 209200.0
- A6 C3 1 0.15260 209200.0
- A6 OH 1 0.13780 209200.0
- A7 C1 1 0.15260 209200.0
- A7 C2 1 0.15260 209200.0
- A7 C3 1 0.15260 209200.0
- Aprime C1 1 0.15260 209200.0
- Abis C1 1 0.15260 209200.0
- Aprime C2 1 0.15260 209200.0
- Aprime C3 1 0.15260 209200.0
- Abis C2 1 0.15260 209200.0
- Abis C3 1 0.15260 209200.0
- Aprime O 1 0.12360 418400.0
- Aprime OH 1 0.12360 418400.0
- Abis Obis 1 0.12230 418400.0
- Aprime N 1 0.13220 418400.0
- Aprime N1 1 0.13220 418400.0
- Aprime N2 1 0.13220 418400.0
- A5 N 1 0.13340 418400.0
- A5 N1 1 0.13340 418400.0
- A5 N2 1 0.13340 418400.0
- A5 C1 1 0.15160 209200.0
- A5 C2 1 0.15160 209200.0
- A5 C3 1 0.15160 209200.0
- A5 A5 1 0.13760 418400.0
- A5 A7 1 0.14510 418400.0
- A5 L5 1 0.13340 418400.0
- A6 O 1 0.12280 418400.0
- A6 O2 1 0.12280 418400.0
- A6 OR 1 0.12280 418400.0
- A6 A6 1 0.13890 418400.0
- A6 A7 1 0.14110 418400.0
- A6 M1 1 0.13350 418400.0
- A6 M2 1 0.13350 418400.0
- A6 M3 1 0.13350 418400.0
- A7 N 1 0.13670 418400.0
- A7 N2 1 0.13670 418400.0
- A7 N1 1 0.13430 418400.0
- A7 A7 1 0.13640 418400.0
- SH H 1 0.13300 209200.0
- S C2 1 0.18080 209200.0
- S C3 1 0.18080 209200.0
- SH C2 1 0.18080 209200.0
- S S 1 0.20150 209200.0
- M1 HN 1 0.10000 209200.0
- M2 HN 1 0.10000 209200.0
- M3 HN 1 0.10000 209200.0
- A6 N 1 0.13550 418400.0
- A6 N1 1 0.13550 418400.0
- A6 N2 1 0.13550 418400.0
- A6 L5 1 0.13550 418400.0
- A6 L6 1 0.13550 418400.0
- A7 L5 1 0.13670 418400.0
- A7 L6 1 0.13670 418400.0
- P OP 1 0.14800 418400.0
- P O2 1 0.15940 209200.0
- Y A6 1 0.13960 418400.0
- Y Aprime 1 0.13960 418400.0
- Y R 1 0.13840 418400.0
- Y W 1 0.13840 418400.0
- Z C2 1 0.15170 209200.0
- Z C3 1 0.15170 209200.0
- Z A6 1 0.14900 418400.0
- Z Aprime 1 0.14900 418400.0
- Z Y 1 0.14440 418400.0
- Z Z 1 0.13570 418400.0
- FE N 1 0.19800 58576.0
- FE N1 1 0.19800 58576.0
- FE N2 1 0.19800 58576.0
- FE W 1 0.19800 58576.0
- OF FE 1 0.16320 58576.0 ; iron-oxygen bond
- OF OF 1 0.12240 418400.0
-
-;[ constrainttypes ]
-
-[ angletypes ]
- ; i j k func th0 cth
- HW OW HW 1 109.47 502.08
- C1 OH HO 1 110.00 502.08
- C2 OH HO 1 110.00 502.08
- C3 OH HO 1 110.00 502.08
- Aprime OH HO 1 110.00 502.08
- A6 OH HO 1 110.00 502.08
- C1 C1 Abis 1 110.10 502.08
- C2 C1 Abis 1 110.10 502.08
- C3 C1 Abis 1 110.10 502.08
- HN N2 HN 1 120.00 502.08
- CP N1 HN 1 119.50 502.08
- CP N2 HN 1 119.50 502.08
- C1 N1 HN 1 119.50 502.08
- C1 N2 HN 1 119.50 502.08
- C2 N1 HN 1 119.50 502.08
- C2 N2 HN 1 119.50 502.08
- C3 N1 HN 1 119.50 502.08
- C3 N2 HN 1 119.50 502.08
- A6 N1 HN 1 119.60 502.08
- A6 N2 HN 1 119.60 502.08
- A5 N1 HN 1 119.60 502.08
- A5 N2 HN 1 119.60 502.08
- A7 N1 HN 1 119.60 502.08
- A7 N2 HN 1 119.60 502.08
- Aprime N1 HN 1 119.60 502.08
- Aprime N2 HN 1 119.60 502.08
- N2 Aprime N2 1 113.00 502.08
- C2 Aprime C3 1 118.00 502.08
- C1 N C1 1 112.40 502.08
- C1 N C2 1 112.40 502.08
- C1 N C3 1 112.40 502.08
- C1 N1 CP 1 112.40 502.08
- C1 N1 C1 1 112.40 502.08
- C1 N1 C2 1 112.40 502.08
- C1 N1 C3 1 112.40 502.08
- C1 N2 CP 1 112.40 502.08
- C1 N2 C1 1 112.40 502.08
- C1 N2 C2 1 112.40 502.08
- C1 N2 C3 1 112.40 502.08
- C2 N C2 1 112.40 502.08
- C2 N C3 1 112.40 502.08
- C2 N1 C2 1 112.40 502.08
- C2 N1 C3 1 112.40 502.08
- C2 N2 C2 1 112.40 502.08
- C2 N2 C3 1 112.40 502.08
- C3 N C3 1 112.40 502.08
- C3 N1 C3 1 112.40 502.08
- C3 N2 C3 1 112.40 502.08
- C1 N CP 1 112.40 502.08
- A6 N C1 1 121.30 502.08
- A6 N C2 1 121.30 502.08
- A6 N C3 1 121.30 502.08
- A6 N1 C1 1 121.30 502.08
- A6 N1 C2 1 121.30 502.08
- A6 N1 C3 1 121.30 502.08
- A6 N2 C1 1 121.30 502.08
- A6 N2 C2 1 121.30 502.08
- A6 N2 C3 1 121.30 502.08
- A5 N C1 1 121.30 502.08
- A5 N C2 1 121.30 502.08
- A5 N C3 1 121.30 502.08
- A5 N1 C1 1 121.30 502.08
- A5 N1 C2 1 121.30 502.08
- A5 N1 C3 1 121.30 502.08
- A5 N2 C1 1 121.30 502.08
- A5 N2 C2 1 121.30 502.08
- A5 N2 C3 1 121.30 502.08
- A7 N C1 1 121.30 502.08
- A7 N C2 1 121.30 502.08
- A7 N C3 1 121.30 502.08
- A7 N1 C1 1 121.30 502.08
- A7 N1 C2 1 121.30 502.08
- A7 N1 C3 1 121.30 502.08
- A7 N2 C1 1 121.30 502.08
- A7 N2 C2 1 121.30 502.08
- A7 N2 C3 1 121.30 502.08
- Aprime N C1 1 121.30 502.08
- Aprime N C2 1 121.30 502.08
- Aprime N C3 1 121.30 502.08
- Aprime N1 C1 1 121.30 502.08
- Aprime N1 C2 1 121.30 502.08
- Aprime N1 C3 1 121.30 502.08
- Aprime N2 C1 1 121.30 502.08
- Aprime N2 C2 1 121.30 502.08
- Aprime N2 C3 1 121.30 502.08
- A5 N A5 1 108.00 1004.16
- A5 N1 A5 1 108.00 1004.16
- A5 N2 A5 1 108.00 1004.16
- A5 N1 A7 1 108.00 1004.16
- H C1 H 1 109.50 502.08
- H C2 H 1 109.50 502.08
- H C3 H 1 109.50 502.08
- H CP H 1 109.50 502.08
- O C1 H 1 109.00 502.08
- OH C1 H 1 109.00 502.08
- OH C2 H 1 109.00 502.08
- OH C3 H 1 109.00 502.08
- O2 C2 H 1 109.00 502.08
- OR C2 H 1 109.00 502.08
- O C1 C1 1 109.50 502.08
- O C1 C2 1 109.50 502.08
- O C1 C3 1 109.50 502.08
- OH C1 C1 1 107.90 502.08
- OH C1 C2 1 107.90 502.08
- OH C1 C3 1 107.90 502.08
- OH C2 C1 1 107.90 502.08
- OH C2 C2 1 107.90 502.08
- OH C2 C3 1 107.90 502.08
- O2 C2 C1 1 109.50 502.08
- O2 C2 C2 1 109.50 502.08
- O2 C2 C3 1 109.50 502.08
- OR C2 C1 1 109.50 502.08
- OR C2 C2 1 109.50 502.08
- OR C2 C3 1 109.50 502.08
- C1 C1 H 1 109.50 502.08
- C1 C2 H 1 109.50 502.08
- C1 C3 H 1 109.50 502.08
- C1 CP H 1 109.50 502.08
- C2 C1 H 1 109.50 502.08
- C2 C2 H 1 109.50 502.08
- C2 C3 H 1 109.50 502.08
- C3 C1 H 1 109.50 502.08
- C3 C2 H 1 109.50 502.08
- C3 C3 H 1 109.50 502.08
- CP C1 H 1 109.50 502.08
- CP CP H 1 109.50 502.08
- N C1 H 1 109.50 502.08
- N C2 H 1 109.50 502.08
- N C3 H 1 109.50 502.08
- N CP H 1 109.50 502.08
- N1 CP H 1 109.50 502.08
- N1 C1 H 1 109.50 502.08
- N1 C2 H 1 109.50 502.08
- N1 C3 H 1 109.50 502.08
- N2 CP H 1 109.50 502.08
- N2 C1 H 1 109.50 502.08
- N2 C2 H 1 109.50 502.08
- N2 C3 H 1 109.50 502.08
- M1 C1 H 1 109.50 502.08
- M1 C2 H 1 109.50 502.08
- M1 C3 H 1 109.50 502.08
- M2 C1 H 1 109.50 502.08
- M2 C2 H 1 109.50 502.08
- M2 C3 H 1 109.50 502.08
- M3 C1 H 1 109.50 502.08
- M3 C2 H 1 109.50 502.08
- M3 C3 H 1 109.50 502.08
- M1 C1 C1 1 111.00 502.08
- M1 C1 C2 1 111.00 502.08
- M1 C1 C3 1 111.00 502.08
- M1 C2 C1 1 111.00 502.08
- M1 C2 C2 1 111.00 502.08
- M1 C2 C3 1 111.00 502.08
- M2 C1 C1 1 111.00 502.08
- M2 C1 C2 1 111.00 502.08
- M2 C1 C3 1 111.00 502.08
- M2 C2 C1 1 111.00 502.08
- M2 C2 C2 1 111.00 502.08
- M2 C2 C3 1 111.00 502.08
- M3 C1 C1 1 111.00 502.08
- M3 C1 C2 1 111.00 502.08
- M3 C1 C3 1 111.00 502.08
- M3 C2 C1 1 111.00 502.08
- M3 C2 C2 1 111.00 502.08
- M3 C2 C3 1 111.00 502.08
- A6 C1 H 1 109.50 502.08
- A6 C2 H 1 109.50 502.08
- A6 C3 H 1 109.50 502.08
- A5 C1 H 1 109.50 502.08
- A5 C2 H 1 109.50 502.08
- A5 C3 H 1 109.50 502.08
- A7 C1 H 1 109.50 502.08
- A7 C2 H 1 109.50 502.08
- A7 C3 H 1 109.50 502.08
- Aprime C1 H 1 109.50 502.08
- Aprime C2 H 1 109.50 502.08
- Aprime C3 H 1 109.50 502.08
- Abis C2 H 1 109.50 502.08
- Abis C3 H 1 109.50 502.08
- Abis C1 H 1 109.50 502.08
- C1 C1 N 1 109.10 502.08
- C1 C1 N1 1 109.10 502.08
- C1 C1 N2 1 109.10 502.08
- C1 C2 N 1 109.10 502.08
- C1 C2 N1 1 109.10 502.08
- C1 C2 N2 1 109.10 502.08
- C2 C1 N 1 109.10 502.08
- C2 C1 N1 1 109.10 502.08
- C2 C1 N2 1 109.10 502.08
- C2 C2 N 1 109.10 502.08
- C2 C2 N1 1 109.10 502.08
- C2 C2 N2 1 109.10 502.08
- C3 C1 N 1 109.10 502.08
- C3 C1 N1 1 109.10 502.08
- C3 C1 N2 1 109.10 502.08
- C3 C2 N 1 109.10 502.08
- C3 C2 N1 1 109.10 502.08
- C3 C2 N2 1 109.10 502.08
- CP C1 N 1 104.00 502.08
- CP C1 N1 1 109.10 502.08
- CP C1 N2 1 109.10 502.08
- A6 C1 N 1 111.30 502.08
- A6 C1 N1 1 111.30 502.08
- A6 C1 N2 1 111.30 502.08
- A6 C2 N 1 111.30 502.08
- A6 C2 N1 1 111.30 502.08
- A6 C2 N2 1 111.30 502.08
- A5 C1 N 1 111.30 502.08
- A5 C1 N1 1 111.30 502.08
- A5 C1 N2 1 111.30 502.08
- A5 C2 N 1 111.30 502.08
- A5 C2 N1 1 111.30 502.08
- A5 C2 N2 1 111.30 502.08
- A7 C1 N 1 111.30 502.08
- A7 C1 N1 1 111.30 502.08
- A7 C1 N2 1 111.30 502.08
- A7 C2 N 1 111.30 502.08
- A7 C2 N1 1 111.30 502.08
- A7 C2 N2 1 111.30 502.08
- Aprime C1 N 1 111.30 502.08
- Aprime C1 N1 1 111.30 502.08
- Aprime C1 N2 1 111.30 502.08
- Aprime C2 N 1 111.30 502.08
- Aprime C2 N1 1 111.30 502.08
- Aprime C2 N2 1 111.30 502.08
- Abis C2 N 1 111.30 502.08
- Abis C2 N1 1 111.30 502.08
- Abis C2 N2 1 111.30 502.08
- A6 C1 M1 1 111.30 502.08
- A6 C1 M2 1 111.30 502.08
- A6 C1 M3 1 111.30 502.08
- A6 C2 M1 1 111.30 502.08
- A6 C2 M2 1 111.30 502.08
- A6 C2 M3 1 111.30 502.08
- A5 C1 M1 1 111.30 502.08
- A5 C1 M2 1 111.30 502.08
- A5 C1 M3 1 111.30 502.08
- A5 C2 M1 1 111.30 502.08
- A5 C2 M2 1 111.30 502.08
- A5 C2 M3 1 111.30 502.08
- A7 C1 M1 1 111.30 502.08
- A7 C1 M2 1 111.30 502.08
- A7 C1 M3 1 111.30 502.08
- A7 C2 M1 1 111.30 502.08
- A7 C2 M2 1 111.30 502.08
- A7 C2 M3 1 111.30 502.08
- Aprime C1 M1 1 111.30 502.08
- Aprime C1 M2 1 111.30 502.08
- Aprime C1 M3 1 111.30 502.08
- Aprime C2 M1 1 111.30 502.08
- Aprime C2 M2 1 111.30 502.08
- Aprime C2 M3 1 111.30 502.08
- Abis C2 M1 1 111.30 502.08
- Abis C2 M2 1 111.30 502.08
- Abis C2 M3 1 111.30 502.08
- Abis C1 M1 1 111.30 502.08
- Abis C1 M2 1 111.30 502.08
- Abis C1 M3 1 111.30 502.08
- Abis C1 N 1 111.30 502.08
- Abis C1 N1 1 111.30 502.08
- Abis C1 N2 1 111.30 502.08
- C1 C1 C1 1 111.40 502.08
- C1 C1 C2 1 111.40 502.08
- C1 C1 C3 1 111.40 502.08
- C1 C2 C1 1 111.40 502.08
- C1 C2 C2 1 111.40 502.08
- C1 C2 C3 1 111.40 502.08
- C1 CP CP 1 107.20 502.08
- C2 C1 C2 1 111.40 502.08
- C2 C1 C3 1 111.40 502.08
- C2 C2 C2 1 111.40 502.08
- C2 C2 C3 1 111.40 502.08
- C3 C1 C3 1 111.40 502.08
- C3 C2 C3 1 111.40 502.08
- CP CP CP 1 103.90 502.08
- N CP CP 1 105.10 502.08
- N1 CP CP 1 105.10 502.08
- N2 CP CP 1 105.10 502.08
- Aprime N CP 1 125.80 502.08
- A6 C1 C1 1 114.10 502.08
- A6 C1 C2 1 114.10 502.08
- A6 C1 C3 1 114.10 502.08
- A6 C2 C1 1 114.10 502.08
- A6 C2 C2 1 114.10 502.08
- A6 C2 C3 1 114.10 502.08
- A5 C1 C1 1 113.90 502.08
- A5 C1 C2 1 113.90 502.08
- A5 C1 C3 1 113.90 502.08
- A5 C2 C1 1 113.90 502.08
- A5 C2 C2 1 113.90 502.08
- A5 C2 C3 1 113.90 502.08
- A7 C1 C1 1 110.10 502.08
- A7 C1 C2 1 110.10 502.08
- A7 C1 C3 1 110.10 502.08
- A7 C2 C1 1 110.10 502.08
- A7 C2 C2 1 110.10 502.08
- A7 C2 C3 1 110.10 502.08
- Aprime C1 C1 1 110.10 502.08
- Aprime C1 C2 1 110.10 502.08
- Aprime C1 C3 1 110.10 502.08
- Aprime C1 CP 1 111.90 502.08
- Abis C1 CP 1 110.10 502.08
- Aprime C2 C1 1 110.10 502.08
- Aprime C2 C2 1 110.10 502.08
- Aprime C2 C3 1 110.10 502.08
- Abis C2 C1 1 110.10 502.08
- Abis C2 C2 1 110.10 502.08
- Abis C2 C3 1 110.10 502.08
- S C2 C1 1 115.50 502.08
- S C2 C2 1 115.50 502.08
- S C2 C3 1 115.50 502.08
- SH C2 C1 1 115.50 502.08
- SH C2 C2 1 115.50 502.08
- SH C2 C3 1 115.50 502.08
- S C2 H 1 110.00 502.08
- S C3 H 1 110.00 502.08
- SH C2 H 1 110.00 502.08
- C2 SH H 1 110.00 502.08
- H A6 H 1 120.00 502.08
- H A5 H 1 120.00 502.08
- H A7 H 1 120.00 502.08
- A6 A6 H 1 120.00 502.08
- A6 A7 H 1 120.00 502.08
- A5 A5 H 1 126.00 502.08
- A5 A7 H 1 120.00 502.08
- A7 A6 H 1 120.00 502.08
- A7 A5 H 1 126.00 502.08
- A7 A7 H 1 120.00 502.08
- O A6 O 1 120.00 502.08
- O Aprime O 1 120.00 502.08
- OH Aprime O 1 120.00 502.08
- O2 A6 O 1 120.00 502.08
- OR A6 O 1 120.00 502.08
- N A6 H 1 120.00 502.08
- N A5 H 1 126.00 502.08
- N A7 H 1 120.00 502.08
- N1 A6 H 1 120.00 502.08
- N1 A5 H 1 126.00 502.08
- N1 A7 H 1 120.00 502.08
- N2 A6 H 1 120.00 502.08
- N2 A5 H 1 126.00 502.08
- N2 A7 H 1 120.00 502.08
- N Aprime O 1 123.50 1004.16
- N1 Aprime O 1 123.50 1004.16
- N2 Aprime O 1 123.50 1004.16
- C1 Aprime O 1 121.00 502.08
- C1 Aprime OH 1 121.00 502.08
- C2 Aprime O 1 121.00 502.08
- C2 Aprime OH 1 121.00 502.08
- C3 Aprime O 1 121.00 502.08
- C3 Aprime C3 1 121.00 502.08
- C1 Aprime N 1 115.50 502.08
- C1 Aprime N1 1 115.50 502.08
- C1 Aprime N2 1 115.50 502.08
- C2 Aprime N 1 115.50 502.08
- C2 Aprime N1 1 115.50 502.08
- C2 Aprime N2 1 115.50 502.08
- C3 Aprime N 1 115.50 502.08
- C3 Aprime N1 1 115.50 502.08
- C3 Aprime N2 1 115.50 502.08
- Obis Abis C1 1 117.70 502.08
- Obis Abis C2 1 117.70 502.08
- Obis Abis C3 1 117.70 502.08
- Obis Abis Obis 1 124.60 1004.16
- C2 A5 A5 1 126.00 502.08
- C2 A5 L5 1 126.00 502.08
- L5 A5 H 1 126.00 502.08
- C2 A5 A7 1 126.00 502.08
- A5 A5 N 1 108.00 1004.16
- A5 A5 N1 1 108.00 1004.16
- A5 A5 N2 1 108.00 1004.16
- A5 A5 L5 1 108.00 1004.16
- N1 A5 L5 1 108.00 1004.16
- C2 A5 N1 1 126.00 502.08
- A7 A5 A5 1 108.00 1004.16
- M1 A6 M1 1 120.00 1004.16
- M1 A6 M2 1 120.00 1004.16
- M1 A6 M3 1 120.00 1004.16
- M2 A6 M2 1 120.00 1004.16
- M2 A6 M3 1 120.00 1004.16
- M3 A6 M3 1 120.00 1004.16
- A6 A6 C1 1 120.10 502.08
- A6 A6 C2 1 120.10 502.08
- A6 A6 C3 1 120.10 502.08
- A6 A6 A6 1 120.00 1004.16
- A6 A6 OH 1 118.40 502.08
- A7 A6 A6 1 120.00 1004.16
- A5 A7 A7 1 108.00 1004.16
- A7 A7 A6 1 120.00 1004.16
- A5 A7 A6 1 132.00 1004.16
- N A7 A6 1 132.00 502.08
- N1 A7 A6 1 132.00 502.08
- N2 A7 A6 1 132.00 502.08
- N1 A7 A7 1 108.00 1004.16
- L5 A7 A6 1 132.00 502.08
- L6 A7 A6 1 132.00 502.08
- C2 S C2 1 99.10 502.08
- C2 S C3 1 99.10 502.08
- S S C2 1 104.30 502.08
- HN M2 HN 1 120.00 502.08
- HN M3 HN 1 109.50 502.08
- C1 M1 HN 1 119.50 502.08
- C1 M2 HN 1 119.50 502.08
- C1 M3 HN 1 109.50 502.08
- C2 M1 HN 1 119.50 502.08
- C2 M2 HN 1 119.50 502.08
- C2 M3 HN 1 109.50 502.08
- C3 M1 HN 1 119.50 502.08
- C3 M2 HN 1 119.50 502.08
- C3 M3 HN 1 109.50 502.08
- A6 M1 HN 1 119.60 502.08
- A6 M2 HN 1 119.60 502.08
- A6 M3 HN 1 119.60 502.08
- A6 M1 C1 1 123.20 502.08
- A6 M1 C2 1 123.20 502.08
- A6 M1 C3 1 123.20 502.08
- A6 M2 C1 1 123.20 502.08
- A6 M2 C2 1 123.20 502.08
- A6 M2 C3 1 123.20 502.08
- A6 M3 C1 1 123.20 502.08
- A6 M3 C2 1 123.20 502.08
- A6 M3 C3 1 123.20 502.08
- A5 L5 A5 1 108.00 1004.16
- A6 N1 A6 1 120.00 502.08
- OH C1 N 1 109.50 502.08
- OH C1 N1 1 109.50 502.08
- OH C1 N2 1 109.50 502.08
- C3 A7 A6 1 108.86 502.08
- C3 A7 A7 1 132.53 502.08
- L5 A7 A7 1 108.00 502.08
- A7 A7 L6 1 120.00 502.08
- A5 L5 A7 1 108.00 502.08
- A6 L5 A7 1 119.33 502.08
- N1 A5 N1 1 108.00 1004.16
- Y A6 H 1 120.00 502.08
- Z C2 H 1 110.00 502.08
- Z C3 H 1 110.00 502.08
- Z A6 H 1 120.00 502.08
- A6 N FE 1 120.00 502.08
- A6 N1 FE 1 120.00 502.08
- A6 N2 FE 1 120.00 502.08
- A5 N FE 1 120.00 502.08
- A5 N1 FE 1 120.00 502.08
- A5 N2 FE 1 120.00 502.08
- A7 N FE 1 120.00 502.08
- A7 N1 FE 1 120.00 502.08
- A7 N2 FE 1 120.00 502.08
- Aprime N FE 1 120.00 502.08
- Aprime N1 FE 1 120.00 502.08
- Aprime N2 FE 1 120.00 502.08
- Y R Y 1 105.40 1004.16
- Y A6 Y 1 124.50 502.08
- Y Aprime Y 1 124.50 502.08
- Y W Y 1 105.40 502.08
- FE W Y 1 127.30 502.08
- R Y A6 1 125.50 1004.16
- R Y Aprime 1 125.50 1004.16
- W Y A6 1 125.20 1004.16
- W Y Aprime 1 125.20 1004.16
- Z Y A6 1 124.20 1004.16
- Z Y Aprime 1 124.20 1004.16
- Z Y R 1 109.50 1004.16
- Z Y W 1 109.50 1004.16
- Y Z C2 1 125.40 502.08
- Y Z C3 1 125.40 502.08
- Y Z A6 1 124.40 1004.16
- Y Z Aprime 1 124.40 1004.16
- Z Z C2 1 127.50 502.08
- Z Z C3 1 127.50 502.08
- Z Z A6 1 128.40 1004.16
- Z Z Aprime 1 128.40 1004.16
- Z Z Y 1 107.00 1004.16
- Z C2 C1 1 109.50 502.08
- Z C2 C2 1 109.50 502.08
- Z C2 C3 1 109.50 502.08
- Z A6 A6 1 120.00 1004.16
- Z A6 A7 1 120.00 1004.16
- W FE N 1 90.00 502.08
- W FE N1 1 90.00 502.08
- W FE N2 1 90.00 502.08
- W FE W 1 180.00 502.08
- OF FE N 1 180.00 502.08
- OF FE N1 1 180.00 502.08
- OF FE N2 1 180.00 502.08
- OF FE W 1 90.00 502.08
- OF OF FE 1 120.00 502.08
-
-
-[ dihedraltypes ]
-; Encad proper dihedrals. Note that there is a difference pf
-; sign in the cosine definition between Gromacs and Encad. All angle values
-; here are thus offset 180 degrees.
- ; i l func q0 cq
- C1 A6 A6 H 1 180.00 167.36 1
- C2 A6 A6 H 1 180.00 167.36 1
- C2 A5 A5 H 1 180.00 167.36 1
- C2 A5 A7 H 1 180.00 167.36 1
- C3 A6 A6 H 1 180.00 167.36 1
- C3 A7 A6 H 1 180.00 167.36 1
- C3 A7 A7 H 1 180.00 167.36 1
- C2 A5 A7 A6 1 180.00 167.36 1
- H A6 N C1 1 180.00 167.36 1
- A6 A6 A6 H 1 0.00 167.36 1
- L5 A7 A7 L5 1 0.00 167.36 1
- L5 A7 A7 L6 1 0.00 167.36 1
- L6 A7 A7 L6 1 0.00 167.36 1
- N A7 A6 A6 1 0.00 167.36 1
- N1 A7 A6 A6 1 0.00 167.36 1
- N2 A7 A6 A6 1 0.00 167.36 1
- N1 A7 A7 A6 1 0.00 167.36 1
- A6 A7 L5 A5 1 180.00 83.68 2
- A7 A7 N1 A5 1 180.00 167.36 1
- Aprime N C1 Aprime 1 0.00 0.00 0 ; will be removed by grompp
- Aprime N C2 Aprime 1 0.00 0.00 0 ; will be removed by grompp
- Aprime N1 C1 Aprime 1 0.00 0.00 0 ; will be removed by grompp
- Aprime N1 C2 Aprime 1 0.00 0.00 0 ; will be removed by grompp
- Aprime N2 C1 Aprime 1 0.00 0.00 0 ; will be removed by grompp
- Aprime N2 C2 Aprime 1 0.00 0.00 0 ; will be removed by grompp
- HN N2 Aprime N2 1 180.00 41.84 2 ; not present in aanahn
- C1 Aprime N C1 1 180.00 41.84 2
- C1 Aprime N C2 1 180.00 41.84 2
- C1 Aprime N C3 1 180.00 41.84 2
- C1 Aprime N1 C1 1 180.00 41.84 2
- C1 Aprime N1 C2 1 180.00 41.84 2
- C1 Aprime N1 C3 1 180.00 41.84 2
- C1 Aprime N2 C1 1 180.00 41.84 2
- C1 Aprime N2 C2 1 180.00 41.84 2
- C1 Aprime N2 C3 1 180.00 41.84 2
- C2 Aprime N C1 1 180.00 41.84 2
- C2 Aprime N C2 1 180.00 41.84 2
- C2 Aprime N C3 1 180.00 41.84 2
- C2 Aprime N1 C1 1 180.00 41.84 2
- C2 Aprime N1 C2 1 180.00 41.84 2
- C2 Aprime N1 C3 1 180.00 41.84 2
- C2 Aprime N2 C1 1 180.00 41.84 2
- C2 Aprime N2 C2 1 180.00 41.84 2
- C2 Aprime N2 C3 1 180.00 41.84 2
- C3 Aprime N C1 1 180.00 41.84 2
- C3 Aprime N C2 1 180.00 41.84 2
- C3 Aprime N C3 1 180.00 41.84 2
- C3 Aprime N1 C1 1 180.00 41.84 2
- C3 Aprime N1 C2 1 180.00 41.84 2
- C3 Aprime N1 C3 1 180.00 41.84 2
- C3 Aprime N2 C1 1 180.00 41.84 2
- C3 Aprime N2 C2 1 180.00 41.84 2
- C3 Aprime N2 C3 1 180.00 41.84 2
- C1 Aprime N1 HN 1 180.00 41.84 2
- C1 Aprime N2 HN 1 180.00 41.84 2
- C2 Aprime N1 HN 1 180.00 41.84 2
- C2 Aprime N2 HN 1 180.00 41.84 2
- C3 Aprime N1 HN 1 180.00 41.84 2
- C3 Aprime N2 HN 1 180.00 41.84 2
- C1 A6 A6 A6 1 0.00 334.72 1
- C2 A6 A6 A6 1 0.00 334.72 1
- C3 A6 A6 A6 1 0.00 334.72 1
- A6 A6 A6 A6 1 180.00 334.72 1
- N C1 CP CP 1 180.00 41.84 1
- N1 C1 CP CP 1 180.00 41.84 1
- N2 C1 CP CP 1 180.00 41.84 1
- C1 Aprime N CP 1 180.00 41.84 2
- C2 Aprime N CP 1 180.00 41.84 2
- C3 Aprime N CP 1 180.00 41.84 2
- Aprime N CP CP 1 0.00 41.84 1
- C1 A6 A6 X 1 180.00 41.84 2
- C2 A6 A6 X 1 180.00 41.84 2
- C2 A5 A5 X 1 180.00 41.84 2
- C2 A5 A7 X 1 180.00 41.84 2
- C3 A6 A6 X 1 180.00 41.84 2
- C3 A7 A6 X 1 180.00 41.84 2
- C3 A7 A7 X 1 180.00 41.84 2
- X A5 N C1 1 0.00 167.36 1
- X A5 N C2 1 0.00 167.36 1
- X A5 N C3 1 0.00 167.36 1
- X A5 N1 C1 1 0.00 167.36 1
- X A5 N1 C2 1 0.00 167.36 1
- X A5 N1 C3 1 0.00 167.36 1
- X A5 N2 C1 1 0.00 167.36 1
- X A5 N2 C2 1 0.00 167.36 1
- X A5 N2 C3 1 0.00 167.36 1
- C2 A5 N1 X 1 0.00 167.36 1
- X A6 N C1 1 0.00 167.36 1
- X A6 N C2 1 0.00 167.36 1
- X A6 N C3 1 0.00 167.36 1
- X A7 N C1 1 180.00 167.36 1
- X A7 N C2 1 180.00 167.36 1
- X A7 N C3 1 180.00 167.36 1
- X A7 N1 C1 1 180.00 167.36 1
- X A7 N1 C2 1 180.00 167.36 1
- X A7 N1 C3 1 180.00 167.36 1
- X A7 N2 C1 1 180.00 167.36 1
- X A7 N2 C2 1 180.00 167.36 1
- X A7 N2 C3 1 180.00 167.36 1
- S S C2 X 1 0.00 0.00 0 ; will be removed by grompp
- X A6 A6 X 1 180.00 167.36 1
- X A6 A7 X 1 180.00 167.36 1
- X A5 A5 X 1 180.00 167.36 1
- X A5 A7 X 1 180.00 167.36 1
- X A7 A7 X 1 180.00 167.36 1
- X A5 N X 1 180.00 334.72 2
- X A5 N1 X 1 180.00 334.72 2
- X A5 N2 X 1 180.00 334.72 2
- X A5 L5 X 1 180.00 41.84 2
- X A6 N X 1 180.00 167.36 1
- X A6 N1 X 1 180.00 167.36 1
- X A6 N2 X 1 180.00 167.36 1
- X A6 L5 X 1 180.00 167.36 1
- X A6 L6 X 1 180.00 167.36 1
- X A7 L5 X 1 180.00 167.36 1
- X A7 L6 X 1 180.00 167.36 1
- X P O2 X 1 0.00 8.368 3
- X P OP X 1 0.00 8.368 3
- X N C1 X 1 0.00 0.00 0 ; will be removed by grompp
- X N C2 X 1 0.00 0.00 0 ; will be removed by grompp
- X N C3 X 1 0.00 0.00 0 ; will be removed by grompp
- X N CP X 1 0.00 0.00 0 ; will be removed by grompp
- X N1 C1 X 1 0.00 0.00 0 ; will be removed by grompp
- X N1 C2 X 1 0.00 0.00 0 ; will be removed by grompp
- X N1 C3 X 1 0.00 0.00 0 ; will be removed by grompp
- X N1 CP X 1 0.00 0.00 0 ; will be removed by grompp
- X N2 C1 X 1 0.00 0.00 0 ; will be removed by grompp
- X N2 C2 X 1 0.00 0.00 0 ; will be removed by grompp
- X N2 C3 X 1 0.00 0.00 0 ; will be removed by grompp
- X N2 CP X 1 0.00 0.00 0 ; will be removed by grompp
- X C1 O X 1 0.00 2.5104 3
- X C1 OH X 1 0.00 2.5104 3
- X C2 OH X 1 0.00 2.5104 3
- X C2 O2 X 1 0.00 2.5104 3
- X C2 OR X 1 0.00 2.5104 3
- X C3 OH X 1 0.00 2.5104 3
- X C1 C1 X 1 0.00 5.8576 3
- X C1 C2 X 1 0.00 5.8576 3
- X C1 C3 X 1 0.00 5.8576 3
- X C2 C2 X 1 0.00 5.8576 3
- X C2 C3 X 1 0.00 5.8576 3
- X C3 C3 X 1 0.00 5.8576 3
- X C1 CP X 1 180.00 5.8576 3
- X CP CP X 1 180.00 5.8576 3
- X C1 Aprime X 1 0.00 0.00 0 ; will be removed by grompp
- X C2 Aprime X 1 0.00 0.00 0 ; will be removed by grompp
- X C3 Aprime X 1 0.00 0.00 0 ; will be removed by grompp
- X CP Aprime X 1 0.00 0.00 0 ; will be removed by grompp
- X C1 A6 X 1 0.00 0.4184 6
- X C1 A5 X 1 0.00 0.4184 6
- X C1 A7 X 1 0.00 0.4184 6
- X C1 Abis X 1 0.00 0.4184 6
- X C2 A6 X 1 0.00 0.4184 6
- X C2 A5 X 1 0.00 0.4184 6
- X C2 A7 X 1 0.00 0.4184 6
- X C2 Abis X 1 0.00 0.4184 6
- X C3 A6 X 1 0.00 0.4184 6
- X C3 A5 X 1 0.00 0.4184 6
- X C3 A7 X 1 0.00 0.4184 6
- X C3 Abis X 1 0.00 0.4184 6
- X C1 M3 X 1 0.00 5.8576 3
- X C2 M3 X 1 0.00 5.8576 3
- X C3 M3 X 1 0.00 5.8576 3
- X A6 O2 X 1 0.00 2.5104 3
- X Aprime OH X 1 0.00 2.5104 3
- X A6 OH X 1 0.00 2.5104 3
- X A6 M1 X 1 180.00 41.84 2
- X A6 M2 X 1 180.00 41.84 2
- X A6 M3 X 1 180.00 41.84 2
- X S C2 X 1 0.00 4.184 3
- X S C3 X 1 0.00 4.184 3
- X SH C2 X 1 0.00 4.184 3
- X S S X 1 0.00 25.104 2
- X M1 C1 X 1 0.00 5.8576 3
- X M1 C2 X 1 0.00 5.8576 3
- X M1 C3 X 1 0.00 5.8576 3
- X M2 C1 X 1 0.00 5.8576 3
- X M2 C2 X 1 0.00 5.8576 3
- X M2 C3 X 1 0.00 5.8576 3
- X Y A6 X 1 180.00 41.84 2
- X Y Aprime X 1 180.00 41.84 2
- X Y R X 1 180.00 83.68 2
- X Y W X 1 180.00 83.68 2
- X Z C2 X 1 0.00 0.4184 6
- X Z C3 X 1 0.00 0.4184 6
- X Z A6 X 1 180.00 41.84 2
- X Z Aprime X 1 180.00 41.84 2
- X Z Y X 1 180.00 83.68 2
- X Z Z X 1 180.00 83.68 2
- X FE N X 1 0.00 0.00 0 ; will be removed by grompp
- X FE N1 X 1 0.00 0.00 0 ; will be removed by grompp
- X FE N2 X 1 0.00 0.00 0 ; will be removed by grompp
- X FE W X 1 0.00 0.00 0 ; will be removed by grompp
- X OF FE X 1 0.00 0.00 0 ; will be removed by grompp
-
-
-
-; Encad out-of-plane potentials are the same functional form as
-; Gromacs proper dihedrals (i.e. cosine, but with shifted sign).
-; Note that the atom order is different too; In Gromacs, the first atom
-; of an improper is the center one, while it is the 3rd in Encad.
-
-; Since they use the same type as proper dihedrals we use defines here
-; to avoid mistakes in ambiguous cases.
-;
-; Note: the three parameters are repeated, to avoid having the free energy B state
-; picked up from the default proper dihedral parameter types
-; (grompp would give errors about non-matching multiplicity between A/B states)
-;
-; DNA
-#define improper_X_X_P_X 180.0 8.368 3 180.0 8.368 3
-#define improper_X_X_M2_X 180.0 8.368 2 180.0 8.368 2
-; Proteins
-#define improper_X_X_N_X 180.0 8.368 2 180.0 8.368 2
-#define improper_X_X_C_X 180.0 8.368 3 180.0 8.368 3
-#define improper_X_X_A_X 180.0 8.368 2 180.0 8.368 2
-#define improper_A_X_C1_X 60.0 75.312 1 60.0 75.312 1
-#define improper_A_X_C1_H -60.0 75.312 1 -60.0 75.312 1
-#define improper_X_X_C1_A 60.0 75.312 1 60.0 75.312 1
-#define improper_C3_C2_C1_C3 60.0 75.312 1 60.0 75.312 1
-#define improper_C_C1_C1_C3 60.0 75.312 1 60.0 75.312 1
-#define improper_C3_C1_C1_OH -60.0 75.312 1 -60.0 75.312 1
-#define improper_C1_C2_C1_C3 -60.0 75.312 1 -60.0 75.312 1
-#define improper_N_A_C1_C -60.0 75.312 1 -60.0 75.312 1
-#define improper_M_A_C1_C -60.0 75.312 1 -60.0 75.312 1
-#define improper_X_X_M_X 180.0 8.368 2 180.0 8.368 2
-#define improper_X_X_M3_X 180.0 8.368 3 180.0 8.368 3
-; Heme
-#define improper_X_X_R_X 180.0 8.368 2 180.0 8.368 2
-#define improper_X_X_W_X 180.0 8.368 2 180.0 8.368 2
-#define improper_X_X_Y_X 180.0 8.368 2 180.0 8.368 2
-#define improper_X_X_Z_X 180.0 8.368 2 180.0 8.368 2
-#define improper_X_X_FE_X 180.0 0.000 4 180.0 0.000 4
-#define improper_X_X_OF_X 180.0 8.368 2 180.0 8.368 2
-
-
-
+++ /dev/null
-[ atomtypes ]
-;name at.num mass charge ptype sigma epsilon
- H 1 1.008 0.0 A 2.54129e-01 1.58992e-01
- O 8 15.9994 0.0 A 2.76223e-01 7.73161e-01
- N 7 14.0027 0.0 A 3.40065e-01 1.72862e+00
- N1 7 14.0027 0.0 A 3.40065e-01 1.72862e+00
- N2 7 14.0027 0.0 A 3.40065e-01 1.72862e+00
- C1 6 12.011 0.0 A 3.84423e-01 3.08863e-01
- C2 6 12.011 0.0 A 3.84423e-01 3.08863e-01
- C3 6 12.011 0.0 A 3.84423e-01 3.08863e-01
- CP 6 12.011 0.0 A 3.84423e-01 3.08863e-01
- A6 6 12.011 0.0 A 3.75977e-01 1.57444e-01
- A5 6 12.011 0.0 A 3.75977e-01 1.57444e-01
- A7 6 12.011 0.0 A 3.75977e-01 1.57444e-01
- Aprime 6 12.011 0.0 A 3.75977e-01 1.57444e-01
- Abis 6 12.011 0.0 A 3.75977e-01 1.57444e-01
- L5 7 14.0027 0.0 A 2.76223e-01 7.73161e-01
- L6 7 14.0027 0.0 A 2.76223e-01 7.73161e-01
- P 15 30.9738 0.0 A 3.84423e-01 3.08863e-01
- OH 8 15.9994 0.0 A 3.16556e-01 7.73161e-01
- O2 8 15.9994 0.0 A 3.16556e-01 7.73161e-01
- OR 8 15.9994 0.0 A 3.16556e-01 7.73161e-01
- S 16 32.060 0.0 A 3.84423e-01 3.08863e-01
- SH 16 32.060 0.0 A 3.84423e-01 3.08863e-01
- M1 7 14.0027 0.0 A 3.40065e-01 1.72862e+00
- M2 7 14.0027 0.0 A 3.40065e-01 1.72862e+00
- M3 7 14.0027 0.0 A 3.40065e-01 1.72862e+00
- HN 1 1.008 0.0 A 4.45449e-02 4.18400e-02
- HO 1 1.008 0.0 A 4.45449e-02 4.18400e-02
- HW 1 1.008 0.0 A 4.45449e-02 4.18400e-02
- CL 17 35.453 0.0 A 4.31068e-01 3.51456e-01
- Obis 8 15.9994 0.0 A 2.76223e-01 7.73161e-01
- OP 8 15.9994 0.0 A 2.76223e-01 7.73161e-01
- R 7 14.0027 0.0 A 3.40065e-01 1.72862e+00
- W 7 14.0027 0.0 A 3.40065e-01 1.72862e+00
- Y 6 12.011 0.0 A 3.75977e-01 1.57444e-01
- Z 6 12.011 0.0 A 3.75977e-01 1.57444e-01
- FE 26 55.847 0.0 A 3.84423e-01 3.08863e-01
- OF 8 15.9994 0.0 A 2.76223e-01 7.73161e-01
- OW 8 15.9994 0.0 A 3.16556e-01 7.73161e-01
- AR 18 39.948 0.0 A 2.54129e-01 1.58992e-01
- NA 11 22.9898 0.0 A 2.40543e-01 7.73161e-01
- MCH3 0 0.0 0.0 A 0.0 0.0
- MNH3 0 0.0 0.0 A 0.0 0.0
- MW 0 0.0 0.0 D 0.0 0.0
-
-[ nonbond_params ]
- ; i j func c6 c12
-; Encad uses strict combination rules, so no need for explicit parameters
-
-[ pairtypes ]
- ; i j func cs6 cs12
-; 1,4 interactions are calculated automatically, using fudge factors.
-; (In the current version, the factors are 0.0, meaning no 1,4 interactions).
-
+++ /dev/null
-[DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges
+++ /dev/null
-#define _FF_ENCAD
-; Implemented from encad library version 25/xi/91,
-; with 1,4 interaction setup modified by Michael Levitt.
-; In this forcefield, both coulombic and Lennard-Jones interactions
-; are completely excluded for 1,4 interaction sites.
-;
-; Vacuum version - scaled down charges.
-
-;
-[ defaults ]
-; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
- 1 3 yes 0.0 0.0
-
-#include "ffnonbonded.itp"
-#include "ffbonded.itp"
-
-
-
-
+++ /dev/null
-f3c F3C flexible three-centered water model
+++ /dev/null
-; This file is for backward compatibility only.
-; Please directly include the file below in your .top file.
-#include "encads.ff/forcefield.itp"
+++ /dev/null
-; This file is for backward compatibility only.
-; Please directly include the file below in your .top file.
-#include "encadv.ff/forcefield.itp"
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff