[gmx-users] Ammonia in Water

[nishap.patel at utoronto.ca]

Hello,

    I created a topology file for 1 ammonia in water. Could someone  
please have a look at the file and let me know if it looks okay.

Thanks
Nisha Patel

; Include forcefield parameters
#include "ffoplsaa.itp"

[ moleculetype ]
; Name            nrexcl
Ammonia             3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass   
typeB    chargeB      massB
      1   opls_237      1    NH3      N      1      -0.76    14.0067    
; qtot -0.76
      2   opls_240      1    NH3     H1      1       0.38      1.008    
; qtot -0.38
      3   opls_240      1    NH3     H2      1       0.38      1.008   ; qtot 0
      4   opls_240      1    NH3     H3      1       0.38      1.008    
; qtot 0.38

[ bonds ]
;  ai    aj funct            c0            c1            c2            c3
     1     2     1
     1     3     1
     1     4     1

[ angles ]
;  ai    aj    ak funct            c0            c1            c2       
       c3
     2     1     3     1
     2     1     4     1
     3     1     4     1

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include water topology
#include "spc.itp"


[ system ]
; Name
ammonia in water

[ molecules ]
; Compound        #mols
Ammonia             1
SOL               345