; ; File 'toluene.top' was generated ; By user: publico (500) ; On host: localhost.localdomain ; At date: Sat Nov 14 12:40:45 2009 ; ; This is your topology file ; "Boom Boom Boom Boom, I Want You in My Room" (Venga Boys) ; ; Include forcefield parameters #include "ffamber94.itp" [ moleculetype ] ; Name nrexcl Protein 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 amber94_11 1 PHEB CB 1 -0.258927 12.01 ; DUM 0.0 12.01 qtot -0.2589 2 amber94_18 1 PHEB HB1 2 0.111837 1.008 ; DUM 0.0 1.008 qtot -0.1471 3 amber94_18 1 PHEB HB2 3 0.112327 1.008 ; DUM 0.0 1.008 qtot -0.03476 4 amber94_3 1 PHEB CG 4 -0.102646 12.01 ; DUM 0.0 12.01 qtot -0.1374 5 amber94_3 1 PHEB CD1 5 -0.07565 12.01 ; DUM 0.0 12.01 qtot -0.2131 6 amber94_22 1 PHEB HD1 6 0.083183 1.008 ; DUM 0.0 1.008 qtot -0.1299 7 amber94_3 1 PHEB CE1 7 -0.092941 12.01 ; DUM 0.0 12.01 qtot -0.2228 8 amber94_22 1 PHEB HE1 8 0.091768 1.008 ; DUM 0.0 1.008 qtot -0.131 9 amber94_3 1 PHEB CZ 9 -0.093685 12.01 ; DUM 0.0 12.01 qtot -0.2247 10 amber94_22 1 PHEB HZ 10 0.091714 1.008 ; DUM 0.0 1.008 qtot -0.133 11 amber94_3 1 PHEB CE2 11 -0.092993 12.01 ; DUM 0.0 12.01 qtot -0.226 12 amber94_22 1 PHEB HE2 12 0.091742 1.008 ; DUM 0.0 1.008 qtot -0.1343 13 amber94_3 1 PHEB CD2 13 -0.075326 12.01 ; DUM 0.0 12.01 qtot -0.2096 14 amber94_22 1 PHEB HD2 14 0.083174 1.008 ; DUM 0.0 1.008 qtot -0.1264 15 amber94_18 1 PHEB HB3 15 0.126422 1.008 ; DUM 0.0 1.008 qtot -9.909e-07 [ bonds ] 1 2 1 1 3 1 1 4 1 1 15 1 4 5 1 4 13 1 5 6 1 5 7 1 7 8 1 7 9 1 9 10 1 9 11 1 11 12 1 11 13 1 13 14 1 [ pairs ] 1 6 1 1 7 1 1 11 1 1 14 1 2 5 1 2 13 1 3 5 1 3 13 1 4 8 1 4 9 1 4 12 1 5 10 1 5 11 1 5 14 1 5 15 1 6 8 1 6 9 1 6 13 1 7 12 1 7 13 1 8 10 1 8 11 1 9 14 1 10 12 1 10 13 1 12 14 1 13 15 1 [ angles ] 2 1 3 1 2 1 4 1 2 1 15 1 3 1 4 1 3 1 15 1 4 1 15 1 1 4 5 1 1 4 13 1 5 4 13 1 4 5 6 1 4 5 7 1 6 5 7 1 5 7 8 1 5 7 9 1 8 7 9 1 7 9 10 1 7 9 11 1 10 9 11 1 9 11 12 1 9 11 13 1 12 11 13 1 4 13 11 1 4 13 14 1 11 13 14 1 [ dihedrals ] 2 1 4 5 3 2 1 4 13 3 3 1 4 5 3 3 1 4 13 3 15 1 4 5 3 15 1 4 13 3 1 4 5 6 3 aromatic_prop_1 1 4 5 7 3 aromatic_prop_1 13 4 5 6 3 aromatic_prop_1 13 4 5 7 3 aromatic_prop_1 1 4 13 11 3 aromatic_prop_1 1 4 13 14 3 aromatic_prop_1 5 4 13 11 3 aromatic_prop_1 5 4 13 14 3 aromatic_prop_1 4 5 7 8 3 aromatic_prop_1 4 5 7 9 3 aromatic_prop_1 6 5 7 8 3 aromatic_prop_1 6 5 7 9 3 aromatic_prop_1 5 7 9 10 3 aromatic_prop_1 5 7 9 11 3 aromatic_prop_1 8 7 9 10 3 aromatic_prop_1 8 7 9 11 3 aromatic_prop_1 7 9 11 12 3 aromatic_prop_1 7 9 11 13 3 aromatic_prop_1 10 9 11 12 3 aromatic_prop_1 10 9 11 13 3 aromatic_prop_1 9 11 13 4 3 aromatic_prop_1 9 11 13 14 3 aromatic_prop_1 12 11 13 4 3 aromatic_prop_1 12 11 13 14 3 aromatic_prop_1 [ dihedrals ] 1 4 13 5 1 4 7 5 6 1 4 11 13 14 1 5 9 7 8 1 7 11 9 10 1 9 13 11 12 1 ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include water topology #include "ffamber_tip3p.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 water [ molecules ] ; Compound #mols Protein 1 SOL 888