; ; File 'agg2.top' was generated ; By user: asd (501) ; On host: ccmb.res.in ; At date: Tue Dec 11 14:27:52 2007 ; ; This is your topology file ; "This Puke Stinks Like Beer" (LIVE) ; ; Include forcefield parameters #include "ffG45a3.itp" [ moleculetype ] ; Name nrexcl Protein 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 NL 1 VAL N 1 -0.83 14.0067 ; qtot -0.83 2 H 1 VAL H1 1 0.415 1.008 ; qtot -0.415 3 H 1 VAL H2 1 0.415 1.008 ; qtot 0 4 CH1 1 VAL CA 2 0 13.019 ; qtot 0 5 CH1 1 VAL CB 2 0 13.019 ; qtot 0 6 CH3 1 VAL CG1 2 0 15.035 ; qtot 0 7 CH3 1 VAL CG2 2 0 15.035 ; qtot 0 8 C 1 VAL C 3 0.38 12.011 ; qtot 0.38 9 O 1 VAL O 3 -0.38 15.9994 ; qtot 0 10 N 2 GLN N 4 -0.28 14.0067 ; qtot -0.28 11 H 2 GLN H 4 0.28 1.008 ; qtot 0 12 CH1 2 GLN CA 5 0 13.019 ; qtot 0 13 CH2 2 GLN CB 5 0 14.027 ; qtot 0 14 CH2 2 GLN CG 5 0 14.027 ; qtot 0 15 C 2 GLN CD 6 0.38 12.011 ; qtot 0.38 16 O 2 GLN OE1 6 -0.38 15.9994 ; qtot 0 17 NT 2 GLN NE2 7 -0.83 14.0067 ; qtot -0.83 18 H 2 GLN HE21 7 0.415 1.008 ; qtot -0.415 19 H 2 GLN HE22 7 0.415 1.008 ; qtot 0 20 C 2 GLN C 8 0.38 12.011 ; qtot 0.38 21 O 2 GLN O 8 -0.38 15.9994 ; qtot 0 22 N 3 ILE N 9 -0.28 14.0067 ; qtot -0.28 23 H 3 ILE H 9 0.28 1.008 ; qtot 0 24 CH1 3 ILE CA 10 0 13.019 ; qtot 0 25 CH1 3 ILE CB 11 0 13.019 ; qtot 0 26 CH2 3 ILE CG1 11 0 14.027 ; qtot 0 27 CH3 3 ILE CG2 11 0 15.035 ; qtot 0 28 CH3 3 ILE CD 11 0 15.035 ; qtot 0 29 C 3 ILE C 12 0.38 12.011 ; qtot 0.38 30 O 3 ILE O 12 -0.38 15.9994 ; qtot 0 31 N 4 VAL N 13 -0.28 14.0067 ; qtot -0.28 32 H 4 VAL H 13 0.28 1.008 ; qtot 0 33 CH1 4 VAL CA 14 0 13.019 ; qtot 0 34 CH1 4 VAL CB 14 0 13.019 ; qtot 0 35 CH3 4 VAL CG1 14 0 15.035 ; qtot 0 36 CH3 4 VAL CG2 14 0 15.035 ; qtot 0 37 C 4 VAL C 15 0.38 12.011 ; qtot 0.38 38 O 4 VAL O 15 -0.38 15.9994 ; qtot 0 39 N 5 TYR N 16 -0.28 14.0067 ; qtot -0.28 40 H 5 TYR H 16 0.28 1.008 ; qtot 0 41 CH1 5 TYR CA 17 0 13.019 ; qtot 0 42 CH2 5 TYR CB 17 0 14.027 ; qtot 0 43 C 5 TYR CG 17 0 12.011 ; qtot 0 44 C 5 TYR CD1 18 -0.1 12.011 ; qtot -0.1 45 HC 5 TYR HD1 18 0.1 1.008 ; qtot 0 46 C 5 TYR CD2 19 -0.1 12.011 ; qtot -0.1 47 HC 5 TYR HD2 19 0.1 1.008 ; qtot 0 48 C 5 TYR CE1 20 -0.1 12.011 ; qtot -0.1 49 HC 5 TYR HE1 20 0.1 1.008 ; qtot 0 50 C 5 TYR CE2 21 -0.1 12.011 ; qtot -0.1 51 HC 5 TYR HE2 21 0.1 1.008 ; qtot 0 52 C 5 TYR CZ 22 0.15 12.011 ; qtot 0.15 53 OA 5 TYR OH 22 -0.548 15.9994 ; qtot -0.398 54 H 5 TYR HH 22 0.398 1.008 ; qtot 0 55 C 5 TYR C 23 0.38 12.011 ; qtot 0.38 56 O 5 TYR O 23 -0.38 15.9994 ; qtot 0 57 N 6 LYSH N 24 -0.28 14.0067 ; qtot -0.28 58 H 6 LYSH H 24 0.28 1.008 ; qtot 0 59 CH1 6 LYSH CA 25 0 13.019 ; qtot 0 60 CH2 6 LYSH CB 25 0 14.027 ; qtot 0 61 CH2 6 LYSH CG 26 0 14.027 ; qtot 0 62 CH2 6 LYSH CD 26 0 14.027 ; qtot 0 63 CH2 6 LYSH CE 27 0.127 14.027 ; qtot 0.127 64 NL 6 LYSH NZ 27 0.129 14.0067 ; qtot 0.256 65 H 6 LYSH HZ1 27 0.248 1.008 ; qtot 0.504 66 H 6 LYSH HZ2 27 0.248 1.008 ; qtot 0.752 67 H 6 LYSH HZ3 27 0.248 1.008 ; qtot 1 68 C 6 LYSH C 28 0.53 12.011 ; qtot 1.53 69 O 6 LYSH OT 28 -0.38 15.9994 ; qtot 1.15 70 OA 6 LYSH O 28 -0.548 15.9994 ; qtot 0.602 71 H 6 LYSH HO 28 0.398 1.008 ; qtot 1 41 55 57 59 1 gd_4 55 57 59 68 1 gd_19 57 59 60 61 1 gd_17 57 59 68 70 1 gd_20 59 60 61 62 1 gd_17 60 61 62 63 1 gd_17 61 62 63 64 1 gd_17 62 63 64 65 1 gd_14 59 68 70 71 1 gd_3 ' ' ' ' ' ' [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 4 1 8 5 2 gi_2 4 6 7 5 2 gi_2 8 4 10 9 2 gi_1 10 8 12 11 2 gi_1 12 10 20 13 2 gi_2 14 17 16 15 2 gi_1 15 19 18 17 2 gi_1 20 12 22 21 2 gi_1 22 20 24 23 2 gi_1 24 22 29 25 2 gi_2 24 27 26 25 2 gi_2 29 24 31 30 2 gi_1 31 29 33 32 2 gi_1 33 31 37 34 2 gi_2 33 35 36 34 2 gi_2 37 33 39 38 2 gi_1 39 37 41 40 2 gi_1 41 39 55 42 2 gi_2 42 46 44 43 2 gi_1 43 44 48 52 2 gi_1 43 46 50 52 2 gi_1 44 43 48 45 2 gi_1 44 43 46 50 2 gi_1 44 48 52 50 2 gi_1 46 43 50 47 2 gi_1 46 43 44 48 2 gi_1 46 50 52 48 2 gi_1 48 52 44 49 2 gi_1 50 52 46 51 2 gi_1 52 48 50 53 2 gi_1 55 41 57 56 2 gi_1 57 55 59 58 2 gi_1 59 57 68 60 2 gi_2 68 59 69 70 2 gi_1 ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include methanol topology #include "methanol.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name Protein in Methanol [ molecules ] ; Compound #mols Protein 1 SOL 335