; ; Topology from .mol2 file ; topolbuild version 1.3 ; Command line: ; /home/sselcuk/gromacs/topolbuild -n molecule -ff oplsaa -dir /home/sselcuk/gromacs/topolbuild1_3/dat/gromacs ; ; The force field files to be included #include "oplsaa.ff/forcefield.itp" [ moleculetype ] ; name nrexcl PC 3 [ atoms ] ; nr type resnr residu atom cgnr charge mass 1 opls_776 1 PC CT 1 -0.36200 12.01100 ; -0.3620000 2 opls_779 1 PC HC 1 0.10400 1.00800 ; -0.2580000 3 opls_779 1 PC HC 1 0.10400 1.00800 ; -0.1540000 4 opls_779 1 PC HC 1 0.10400 1.00800 ; -0.0500000 5 opls_775 1 PC CT 2 0.40100 12.01100 ; 0.3510000 6 opls_778 1 PC HC 2 0.00200 1.00800 ; 0.3530000 7 opls_774 1 PC CT 3 0.16600 12.01100 ; 0.5190000 8 opls_777 1 PC HC 3 0.03000 1.00800 ; 0.5490000 9 opls_777 1 PC HC 3 0.03000 1.00800 ; 0.5790000 10 opls_773 1 PC OS 3 -0.44200 15.99940 ; 0.1370000 11 opls_772 1 PC C 4 0.85700 12.01100 ; 0.9940000 12 opls_771 1 PC O 4 -0.51000 15.99940 ; 0.4840000 13 opls_773 1 PC OS 2 -0.48400 15.99940 ; 0.0000000 ; total molecule charge = 0.0000000 [ bonds ] ; ai aj funct b0 kb 1 5 1 0.15290 224262. ; CT- CT 1 2 1 0.10900 284512. ; CT- HC 1 3 1 0.10900 284512. ; CT- HC 1 4 1 0.10900 284512. ; CT- HC 5 6 1 0.10900 284512. ; CT- HC 5 13 1 0.14100 267776. ; CT- OS 5 7 1 0.15290 224262. ; CT- CT 7 10 1 0.14100 267776. ; CT- OS 7 8 1 0.10900 284512. ; CT- HC 7 9 1 0.10900 284512. ; CT- HC 10 11 ; OS- C 11 12 ; C- O 11 13 ; C- OS [ pairs ] 2 6 1 ; HC- HC 2 13 1 ; HC- OS 2 7 1 ; HC- CT 3 6 1 ; HC- HC 3 13 1 ; HC- OS 3 7 1 ; HC- CT 4 6 1 ; HC- HC 4 13 1 ; HC- OS 4 7 1 ; HC- CT 1 11 1 ; CT- C 6 11 1 ; HC- C 1 10 1 ; CT- OS 1 8 1 ; CT- HC 1 9 1 ; CT- HC 6 10 1 ; HC- OS 6 8 1 ; HC- HC 6 9 1 ; HC- HC 13 8 1 ; OS- HC 13 9 1 ; OS- HC 8 11 1 ; HC- C 9 11 1 ; HC- C 7 12 1 ; CT- O 12 5 1 ; O- CT [ angles ] ; ai aj ak funct th0 cth 2 1 5 1 110.700 313.8000 ; HC- CT- CT 3 1 5 1 110.700 313.8000 ; HC- CT- CT 4 1 5 1 110.700 313.8000 ; HC- CT- CT 1 5 6 1 110.700 313.8000 ; CT- CT- HC 1 5 13 1 109.500 418.4000 ; CT- CT- OS 1 5 7 1 112.700 488.2730 ; CT- CT- CT 3 1 2 1 107.800 276.1440 ; HC- CT- HC 4 1 2 1 107.800 276.1440 ; HC- CT- HC 4 1 3 1 107.800 276.1440 ; HC- CT- HC 13 5 6 1 109.500 292.8800 ; OS- CT- HC 7 5 6 1 110.700 313.8000 ; CT- CT- HC 7 5 13 1 109.500 418.4000 ; CT- CT- OS 5 13 11 ; CT- OS- C 5 7 10 1 109.500 418.4000 ; CT- CT- OS 5 7 8 1 110.700 313.8000 ; CT- CT- HC 5 7 9 1 110.700 313.8000 ; CT- CT- HC 8 7 10 1 109.500 292.8800 ; HC- CT- OS 9 7 10 1 109.500 292.8800 ; HC- CT- OS 7 10 11 ; CT- OS- C 9 7 8 1 107.800 276.1440 ; HC- CT- HC 10 11 12 ; OS- C- O 10 11 13 ; OS- C- OS 13 11 12 ; OS- C- O [ dihedrals ] ; ai aj ak al funct phi0 cp mult 7 5 13 11 ; dih CT- CT- OS- C 5 7 10 11 ; dih CT- CT- OS- C 7 10 11 13 ; dih CT- OS- C- OS 10 11 13 5 ; dih OS- C- OS- CT [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 c4 c5 2 1 5 13 3 0.97905 2.93716 0.00000 -3.91622 0.00000 0.00000 ; dih HC- CT- CT- OS 13 5 7 10 3 -1.15060 1.15060 0.00000 0.00000 0.00000 0.00000 ; dih OS- CT- CT- OS [ dihedrals ] ; ai aj ak al funct phi0 cp mult 11 10 12 13 1 180.000 1.100 2 ; imp C- OS- O- OS ; Include Position restraint file ; WARNING: Position restraints and distance restraints ought not be done together #ifdef POSRES #include "posremolecule.itp" #endif ; Include water topology #include "spce.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 ] ; title from mol2 input ZINC01481909 [ molecules ] ; molecule name nr. ZINC01481909 1