;	This is your topology file
;	Phenylalanine side chain (no backbone present in the file)
;
; Include forcefield parameters
#include "ffG43a2.itp"

[ moleculetype ]
; Name            nrexcl
Protein             3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB      massB
     1        CH3      1    PHE     CB      1          0     15.035    DUM     0        15.035
     2          C      1    PHE     CG      1          0     12.011    DUM     0        12.011
     3          C      1    PHE    CD1      2       -0.1     12.011    DUM     0        12.011
     4         HC      1    PHE    HD1      2        0.1      1.008    DUM     0         1.008
     5          C      1    PHE    CD2      3       -0.1     12.011    DUM     0        12.011
     6         HC      1    PHE    HD2      3        0.1      1.008    DUM     0         1.008
     7          C      1    PHE    CE1      4       -0.1     12.011    DUM     0        12.011
     8         HC      1    PHE    HE1      4        0.1      1.008    DUM     0         1.008
     9          C      1    PHE    CE2      5       -0.1     12.011    DUM     0        12.011
    10         HC      1    PHE    HE2      5        0.1      1.008    DUM     0         1.008
    11          C      1    PHE     CZ      6       -0.1     12.011    DUM     0        12.011
    12         HC      1    PHE     HZ      6        0.1      1.008    DUM     0         1.008

[ bonds ]
;  ai    aj funct            c0            c1            c2            c3
    1     2     2    gb_26    gb_26
    2     3     2    gb_15    gb_15
    2     5     2    gb_15    gb_15
    3     4     2    gb_3     gb_3
    3     7     2    gb_15    gb_15
    5     6     2    gb_3     gb_3
    5     9     2    gb_15    gb_15
    7     8     2    gb_3     gb_3
    7    11     2    gb_15    gb_15
    9    10     2    gb_3     gb_3
    9    11     2    gb_15    gb_15
   11    12     2    gb_3     gb_3

[ angles ]
;  ai    aj    ak funct            c0            c1            c2            c3
    1     2     3     2    ga_26   ga_26
    1     2     5     2    ga_26   ga_26
    3     2     5     2    ga_26   ga_26
    2     3     4     2    ga_24   ga_24
    2     3     7     2    ga_26   ga_26
    4     3     7     2    ga_24   ga_24
    2     5     6     2    ga_24   ga_24
    2     5     9     2    ga_26   ga_26
    6     5     9     2    ga_24   ga_24
    3     7     8     2    ga_24   ga_24
    3     7    11     2    ga_26   ga_26
    8     7    11     2    ga_24   ga_24
    5     9    10     2    ga_24   ga_24
    5     9    11     2    ga_26   ga_26
   10     9    11     2    ga_24   ga_24
    7    11     9     2    ga_26   ga_26
    7    11    12     2    ga_24   ga_24
    9    11    12     2    ga_24   ga_24

[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1            c2            c3
    1     5     3     2     2    gi_1   gi_1
    2     3     7    11     2    gi_1   gi_1
    2     5     9    11     2    gi_1   gi_1
    3     2     7     4     2    gi_1   gi_1
    3     2     5     9     2    gi_1   gi_1
    3     7    11     9     2    gi_1   gi_1
    5     2     9     6     2    gi_1   gi_1
    5     2     3     7     2    gi_1   gi_1
    5     9    11     7     2    gi_1   gi_1
    7    11     3     8     2    gi_1   gi_1
    9    11     5    10     2    gi_1   gi_1
   11     7     9    12     2    gi_1   gi_1

; 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
Phenylalanine side chain (no backbone present in the file) in water

[ molecules ]
; Compound        #mols
Protein             1