[gmx-users] ethanol bond types

[nishap.patel at utoronto.ca]

Hello,

     I am trying to simulate Ethanol in water using OPLSAA. I already  
tried it with all atoms, but now I want to try it with United atoms  
for ethanol, i.e. CH3,CH2,OH, and HO in my topology file. I created  
the topology but I got an error saying 'No bond types', so I checked  
ffoplsaabon.itp file, and as the error indicated I could not find any  
bond types. Is there a way for me to determine the bonds? This is my  
topology file for ethanol:

[ moleculetype ]
; Name            nrexcl
Ethanol             3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass   
typeB    chargeB      massB
      1   opls_068      1    EOH     CB      1          0     15.035   ; qtot 0
      2   opls_081      1    EOH     CA      2      0.265     14.027    
; qtot 0.265
      3   opls_078      1    EOH     OH      2       -0.7    15.9994    
; qtot -0.435
      4   opls_079      1    EOH     HO      2      0.435      1.008   ; qtot 0

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

[ pairs ]
;  ai    aj funct            c0            c1            c2            c3
     1     4     1

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

[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1             
c2            c3            c4            c5
     1     2     3     4     3

I checked one of the paper that has been published using the same  
parameters as follows:

    Table 1. Potential Parameters and Molecular
          Geometries of OPLS-UA and SPC/E
                                              qa
atom or group       ?, Å      , kJ/mol
                          OPLS
      R1            3.905      0.7322        0.000
      R2            3.905      0.4937        0.265
                                           -0.700
      O             3.070      0.7113
      H             0.000      0.0000        0.435

I would really appreciate some suggestions, on how I should tackle the error.

Thanks

Nisha P