; FEP for a buried water molecule
; by: ssomani 

#include "ffoplsaa.itp"

--------- new definitions. ssomani ------------------------------
[ atomtypes ]
 opls_OW   OZ      15.99940    -0.820       A    3.16557e-01  6.50629e-01
 opls_HW   HZH      1.00800     0.410       A    0.00000e+00  0.00000e+00
opls_OWm   OZ      15.99940    -0.820       A    0.00000e-01  6.50629e-01
opls_HWm   HZH      1.00800     0.410       A    0.00000e+00  0.00000e+00

[ bondtypes ]
 OZ  HZH    1    0.1     345000  ; OH bond 

[ angletypes ]
 HZH   OZ    HZH     1   109.47  383   ; 

;------ssomani------------------------------------

[ moleculetype ]
; Name            nrexcl
Protein             3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB      massB
     1   opls_287      1    ALA      N      1       -0.3    14.0067   ; qtot -0.3
     2   opls_290      1    ALA     H1      1       0.33      1.008   ; qtot 0.03
     :  	
     :
  2436   opls_272    153    SER     O1    851       -0.8    15.9994   ; qtot -0.2
  2437   opls_272    153    SER     O2    851       -0.8    15.9994   ; qtot -1
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB      massB

[ bonds ]
;  ai    aj funct            c0            c1            c2            c3
    1     2     1 
    1     3     1 
    1     4     1 
    :     :     : 
 2433  2434     1 
 2435  2436     1 
 2435  2437     1 

[ pairs ]
;  ai    aj funct            c0            c1            c2            c3
    1     8     1 
    1     9     1 
    1    10     1 
    :     :
 2432  2434     1 
 2432  2435     1 
 2433  2435     1 

[ angles ]
;  ai    aj    ak funct            c0            c1            c2            c3
    2     1     3     1 
    2     1     4     1 
    2     1     5     1 
    3     1     4     1 
    :     : 	
 2428  2435  2436     1 
 2428  2435  2437     1 
 2436  2435  2437     1 

[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1            c2            c3            c4            c5
    2     1     5     6     3 
    2     1     5     7     3 
    :     :	
 2431  2430  2433  2434     3 
 2432  2430  2433  2434     3 

[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1            c2            c3
    5    13    11    12     1    improper_O_C_X_Y
    :     :
 2424  2428  2426  2427     1    improper_Z_N_X_Y
 2428  2436  2435  2437     1    improper_O_C_X_Y

;------define a SPC water ssomani------------------
[ moleculetype ]
; Name     nrexcl
HOH          2

[ atoms ]
;   nr       type  resnr residue  atom   cgnr    charge     mass        typeB    chargeB      massB
     1   opls_OW       1    HOH     OZ    1      -0.820    15.9994     opls_OWm   0.00    15.9994
     2   opls_HW       1    HOH    HZH    1       0.410     1.0080     opls_HWm   0.00     1.0080
     3   opls_HW       1    HOH    HZH    1       0.410     1.0080     opls_HWm   0.00     1.0080
 
[ bonds ] 
;  ai    aj funct            c0            c1            c2            c3
    1     2     1             
    1     3     1             
 
[ angles ] 
;  ai    aj    ak funct            c0            c1            c2            c3
    2     1     3     1   
;------water defined. ssomani---------------------


; 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 in water t= 2000.00012

[ molecules ]
; Compound        #mols
Protein             1
HOH                 1 ; ssomani
SOL              7172
NA+                1