; ; File 'topol.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Tue Aug 24 16:46:10 2010 ; ; This is your topology file ; it was generated using program: ; pdb2gmx - version 4.5-beta3 ; with command line: ; ../../../bin/pdb2gmx -f IWV.pdb ; ; Include forcefield parameters #include "gromos53a6.ff/forcefield.itp" [ moleculetype ] ; Name nrexcl Protein_chain_A 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 33 LEU rtp LEU q +1.0 1 NL 33 LEU N 1 0.129 14.0067 ; qtot 0.129 2 H 33 LEU H1 1 0.248 1.008 ; qtot 0.377 3 H 33 LEU H2 1 0.248 1.008 ; qtot 0.625 4 H 33 LEU H3 1 0.248 1.008 ; qtot 0.873 5 CH1 33 LEU CA 2 0.127 13.019 ; qtot 1 6 CH2 33 LEU CB 2 0 14.027 ; qtot 1 7 CH1 33 LEU CG 3 0 13.019 ; qtot 1 8 CH3 33 LEU CD1 3 0 15.035 ; qtot 1 9 CH3 33 LEU CD2 3 0 15.035 ; qtot 1 10 C 33 LEU C 4 0.45 12.011 ; qtot 1.45 11 O 33 LEU O 4 -0.45 15.9994 ; qtot 1 ; residue 34 TRP rtp TRP q 0.0 12 N 34 TRP N 5 -0.31 14.0067 ; qtot 0.69 13 H 34 TRP H 5 0.31 1.008 ; qtot 1 14 CH1 34 TRP CA 6 0 13.019 ; qtot 1 15 CH2 34 TRP CB 6 0 14.027 ; qtot 1 16 C 34 TRP CG 7 -0.21 12.011 ; qtot 0.79 17 C 34 TRP CD1 7 -0.14 12.011 ; qtot 0.65 18 HC 34 TRP HD1 7 0.14 1.008 ; qtot 0.79 19 C 34 TRP CD2 7 0 12.011 ; qtot 0.79 20 NR 34 TRP NE1 7 -0.1 14.0067 ; qtot 0.69 21 H 34 TRP HE1 7 0.31 1.008 ; qtot 1 22 C 34 TRP CE2 7 0 12.011 ; qtot 1 23 C 34 TRP CE3 8 -0.14 12.011 ; qtot 0.86 24 HC 34 TRP HE3 8 0.14 1.008 ; qtot 1 25 C 34 TRP CZ2 9 -0.14 12.011 ; qtot 0.86 26 HC 34 TRP HZ2 9 0.14 1.008 ; qtot 1 27 C 34 TRP CZ3 10 -0.14 12.011 ; qtot 0.86 28 HC 34 TRP HZ3 10 0.14 1.008 ; qtot 1 29 C 34 TRP CH2 11 -0.14 12.011 ; qtot 0.86 30 HC 34 TRP HH2 11 0.14 1.008 ; qtot 1 31 C 34 TRP C 12 0.45 12.011 ; qtot 1.45 32 O 34 TRP O 12 -0.45 15.9994 ; qtot 1 ; residue 35 VAL rtp VAL q -1.0 33 N 35 VAL N 13 -0.31 14.0067 ; qtot 0.69 34 H 35 VAL H 13 0.31 1.008 ; qtot 1 35 CH1 35 VAL CA 14 0 13.019 ; qtot 1 36 CH1 35 VAL CB 14 0 13.019 ; qtot 1 37 CH3 35 VAL CG1 14 0 15.035 ; qtot 1 38 CH3 35 VAL CG2 14 0 15.035 ; qtot 1 39 C 35 VAL C 15 0.27 12.011 ; qtot 1.27 40 OM 35 VAL O1 15 -0.635 15.9994 ; qtot 0.635 41 OM 35 VAL O2 15 -0.635 15.9994 ; qtot 0 [ bonds ] ; ai aj funct c0 c1 c2 c3 1 2 2 gb_2 1 3 2 gb_2 1 4 2 gb_2 1 5 2 gb_21 5 6 2 gb_27 5 10 2 gb_27 6 7 2 gb_27 7 8 2 gb_27 7 9 2 gb_27 10 11 2 gb_5 10 12 2 gb_10 12 13 2 gb_2 12 14 2 gb_21 14 15 2 gb_27 14 31 2 gb_27 15 16 2 gb_27 16 17 2 gb_10 16 19 2 gb_16 17 18 2 gb_3 17 20 2 gb_10 19 22 2 gb_16 19 23 2 gb_16 20 21 2 gb_2 20 22 2 gb_10 22 25 2 gb_16 23 24 2 gb_3 23 27 2 gb_16 25 26 2 gb_3 25 29 2 gb_16 27 28 2 gb_3 27 29 2 gb_16 29 30 2 gb_3 31 32 2 gb_5 31 33 2 gb_10 33 34 2 gb_2 33 35 2 gb_21 35 36 2 gb_27 35 39 2 gb_27 36 37 2 gb_27 36 38 2 gb_27 39 40 2 gb_6 39 41 2 gb_6 [ pairs ] ; ai aj funct c0 c1 c2 c3 1 7 1 1 11 1 1 12 1 2 6 1 2 10 1 3 6 1 3 10 1 4 6 1 4 10 1 5 8 1 5 9 1 5 13 1 5 14 1 6 11 1 6 12 1 7 10 1 10 15 1 10 31 1 11 13 1 11 14 1 12 16 1 12 32 1 12 33 1 13 15 1 13 31 1 14 17 1 14 19 1 14 34 1 14 35 1 15 32 1 15 33 1 16 31 1 31 36 1 31 39 1 32 34 1 32 35 1 33 37 1 33 38 1 33 40 1 33 41 1 34 36 1 34 39 1 36 40 1 36 41 1 37 39 1 38 39 1 [ angles ] ; ai aj ak funct c0 c1 c2 c3 2 1 3 2 ga_10 2 1 4 2 ga_10 2 1 5 2 ga_11 3 1 4 2 ga_10 3 1 5 2 ga_11 4 1 5 2 ga_11 1 5 6 2 ga_13 1 5 10 2 ga_13 6 5 10 2 ga_13 5 6 7 2 ga_15 6 7 8 2 ga_15 6 7 9 2 ga_15 8 7 9 2 ga_15 5 10 11 2 ga_30 5 10 12 2 ga_19 11 10 12 2 ga_33 10 12 13 2 ga_32 10 12 14 2 ga_31 13 12 14 2 ga_18 12 14 15 2 ga_13 12 14 31 2 ga_13 15 14 31 2 ga_13 14 15 16 2 ga_15 15 16 17 2 ga_37 15 16 19 2 ga_37 17 16 19 2 ga_7 16 17 18 2 ga_36 16 17 20 2 ga_7 18 17 20 2 ga_36 16 19 22 2 ga_7 16 19 23 2 ga_39 22 19 23 2 ga_27 17 20 21 2 ga_36 17 20 22 2 ga_7 21 20 22 2 ga_36 19 22 20 2 ga_7 19 22 25 2 ga_27 20 22 25 2 ga_39 19 23 24 2 ga_25 19 23 27 2 ga_27 24 23 27 2 ga_25 22 25 26 2 ga_25 22 25 29 2 ga_27 26 25 29 2 ga_25 23 27 28 2 ga_25 23 27 29 2 ga_27 28 27 29 2 ga_25 25 29 27 2 ga_27 25 29 30 2 ga_25 27 29 30 2 ga_25 14 31 32 2 ga_30 14 31 33 2 ga_19 32 31 33 2 ga_33 31 33 34 2 ga_32 31 33 35 2 ga_31 34 33 35 2 ga_18 33 35 36 2 ga_13 33 35 39 2 ga_13 36 35 39 2 ga_13 35 36 37 2 ga_15 35 36 38 2 ga_15 37 36 38 2 ga_15 35 39 40 2 ga_22 35 39 41 2 ga_22 40 39 41 2 ga_38 [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 c4 c5 2 1 5 10 1 gd_29 1 5 6 7 1 gd_34 1 5 10 12 1 gd_40 5 6 7 8 1 gd_34 5 10 12 14 1 gd_14 10 12 14 31 1 gd_39 12 14 15 16 1 gd_34 12 14 31 33 1 gd_40 14 15 16 19 1 gd_40 14 31 33 35 1 gd_14 31 33 35 39 1 gd_39 33 35 36 37 1 gd_34 33 35 39 41 1 gd_40 [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 5 1 10 6 2 gi_2 6 8 9 7 2 gi_2 10 5 12 11 2 gi_1 12 10 14 13 2 gi_1 14 12 31 15 2 gi_2 15 19 17 16 2 gi_1 16 23 22 19 2 gi_1 16 19 22 20 2 gi_1 16 17 20 22 2 gi_1 17 16 20 18 2 gi_1 17 20 22 19 2 gi_1 17 16 19 22 2 gi_1 19 16 17 20 2 gi_1 19 22 25 29 2 gi_1 19 23 27 29 2 gi_1 20 17 22 21 2 gi_1 20 25 19 22 2 gi_1 22 19 23 27 2 gi_1 22 25 29 27 2 gi_1 23 19 27 24 2 gi_1 23 19 22 25 2 gi_1 23 27 29 25 2 gi_1 25 22 29 26 2 gi_1 27 23 29 28 2 gi_1 29 25 27 30 2 gi_1 31 14 33 32 2 gi_1 33 31 35 34 2 gi_1 35 33 39 36 2 gi_2 35 37 38 36 2 gi_2 39 35 41 40 2 gi_1 ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include water topology #include "gromos53a6.ff/spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "gromos53a6.ff/ions.itp" [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein_chain_A 1