; ; File 'di.top' was generated ; By user: ndhumal (36026) ; On host: c22 ; At date: Tue Nov 17 08:27:33 2009 ; ; This is your topology file ; "Move about like a Scientist, lay down, get kissed" (Red Hot Chili Peppars) ; ; Include forcefield parameters #include "ffoplsaa.itp" [ moleculetype ] ; Name nrexcl Protein 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_186 1 PCD O 1 -0.3088 15.9994 ; qtot -0.3088 2 opls_263 1 PCD C2 2 0.2336 12.011 ; qtot -0.0752 3 opls_263 1 PCD C3 2 0.2336 12.011 ; qtot 0.1584 4 opls_186 1 PCD O4 3 -0.3088 15.9994 ; qtot -0.1504 5 opls_263 1 PCD C5 4 0.2336 12.011 ; qtot 0.0832 6 opls_263 1 PCD C6 4 0.2336 12.011 ; qtot 0.3168 7 opls_263 1 PCD C7 4 -0.2325 12.011 ; qtot 0.0843 8 opls_263 1 PCD C8 4 0.0907 12.011 ; qtot 0.175 9 opls_263 1 PCD C9 4 0.0908 12.011 ; qtot 0.2658 10 opls_263 1 PCD C10 4 -0.2326 12.011 ; qtot 0.0332 11 opls_263 1 PCD C11 4 -0.2326 12.011 ; qtot -0.1994 12 opls_263 1 PCD C12 4 0.0907 12.011 ; qtot -0.1087 13 opls_263 1 PCD C13 4 0.0907 12.011 ; qtot -0.018 14 opls_263 1 PCD C14 4 -0.2325 12.011 ; qtot -0.2505 15 opls_264 1 PCD CL1 5 -0.0986 35.453 ; qtot -0.3491 16 opls_264 1 PCD CL2 5 -0.0986 35.453 ; qtot -0.4477 17 opls_264 1 PCD CL3 5 -0.0986 35.453 ; qtot -0.5463 18 opls_264 1 PCD CL4 5 -0.0986 35.453 ; qtot -0.6449 19 opls_146 1 PCD H19 6 0.1612 1.008 ; qtot -0.4837 20 opls_146 1 PCD H20 6 0.1612 1.008 ; qtot -0.3225 21 opls_146 1 PCD H21 6 0.1612 1.008 ; qtot -0.1613 22 opls_146 1 PCD H22 6 0.1612 1.008 ; qtot -0.0001 [ bonds ] ; ai aj funct c0 c1 c2 c3 1 2 1 1 6 1 2 3 1 2 10 1 3 4 1 3 7 1 4 5 1 5 6 1 5 11 1 6 14 1 7 8 1 7 20 1 8 9 1 8 15 1 9 10 1 9 16 1 10 19 1 11 12 1 11 22 1 12 13 1 12 18 1 13 14 1 13 18 1 14 21 1 [ pairs ] ; ai aj funct c0 c1 c2 c3 1 4 1 1 7 1 1 9 1 1 11 1 1 13 1 1 19 1 1 21 1 2 5 1 2 8 1 2 14 1 2 16 1 2 20 1 3 6 1 3 9 1 3 11 1 3 15 1 3 19 1 4 8 1 4 10 1 4 12 1 4 14 1 4 20 1 4 22 1 5 7 1 5 13 1 5 18 1 5 21 1 6 10 1 6 12 1 6 18 1 6 22 1 7 10 1 7 16 1 8 19 1 9 20 1 10 15 1 11 14 1 12 21 1 13 22 1 15 16 1 15 20 1 16 19 1 18 21 1 18 22 1 [ angles ] ; ai aj ak funct c0 c1 c2 c3 2 1 6 1 1 2 3 1 1 2 10 1 3 2 10 1 2 3 4 1 2 3 7 1 4 3 7 1 3 4 5 1 4 5 6 1 4 5 11 1 6 5 11 1 1 6 5 1 1 6 14 1 5 6 14 1 3 7 8 1 3 7 20 1 8 7 20 1 7 8 9 1 7 8 15 1 9 8 15 1 8 9 10 1 8 9 16 1 10 9 16 1 2 10 9 1 2 10 19 1 9 10 19 1 5 11 12 1 5 11 22 1 12 11 22 1 11 12 13 1 11 12 18 1 13 12 18 1 12 13 14 1 12 13 18 1 14 13 18 1 6 14 13 1 6 14 21 1 13 14 21 1 12 18 13 1 [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 c4 c5 6 1 2 3 3 6 1 2 10 3 2 1 6 5 3 2 1 6 14 3 1 2 3 4 3 1 2 3 7 3 10 2 3 4 3 10 2 3 7 3 1 2 10 9 3 1 2 10 19 3 3 2 10 9 3 3 2 10 19 3 2 3 4 5 3 7 3 4 5 3 2 3 7 8 3 2 3 7 20 3 4 3 7 8 3 4 3 7 20 3 3 4 5 6 3 3 4 5 11 3 4 5 6 1 3 4 5 6 14 3 11 5 6 1 3 11 5 6 14 3 4 5 11 12 3 4 5 11 22 3 6 5 11 12 3 6 5 11 22 3 1 6 14 13 3 1 6 14 21 3 5 6 14 13 3 5 6 14 21 3 3 7 8 9 3 3 7 8 15 3 20 7 8 9 3 20 7 8 15 3 7 8 9 10 3 7 8 9 16 3 15 8 9 10 3 15 8 9 16 3 8 9 10 2 3 8 9 10 19 3 16 9 10 2 3 16 9 10 19 3 5 11 12 13 3 5 11 12 18 3 22 11 12 13 3 22 11 12 18 3 11 12 13 14 3 11 12 13 18 3 18 12 13 14 3 11 12 18 13 3 12 13 14 6 3 12 13 14 21 3 18 13 14 6 3 18 13 14 21 3 14 13 18 12 3 ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include water topology #include "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 generic topology for ions #include "ions.itp" [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein 1