[gmx-users] Create gro and top file for hexanoic acid

[cuong nguyen]

Dear Sir/Madam,

I have tried to creat the gro and top file for acid hexanoic by using the
PRODRG server. However, the atom H in -COOH group could not be found and
two O atoms are the same.

[ moleculetype ]
; Name nrexcl
DRG      3

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1        OM     1  DRG     OAB     1   -0.767  15.9994
     2           C     1  DRG     CAI       1    0.343  12.0110
     3        OM     1  DRG     OAC     1   -0.766  15.9994
     4       CH2     1  DRG     CAH     1    0.048  14.0270
     5       CH2     1  DRG     CAG     1    0.047  14.0270
     6       CH2     1  DRG     CAF     1    0.047  14.0270
     7       CH2     1  DRG     CAE     1    0.048  14.0270
     8       CH2     1  DRG     CAD     2    0.000  14.0270
     9       CH3     1  DRG     CAA     3    0.000  15.0350

[ bonds ]
; ai  aj  fu    c0, c1, ...
   2   1   2    0.125  13400000.0    0.125  13400000.0 ;   CAI  OAB
   2   3   2    0.125  13400000.0    0.125  13400000.0 ;   CAI  OAC
   2   4   2    0.153   7150000.0    0.153   7150000.0 ;   CAI  CAH
   4   5   2    0.153   7150000.0    0.153   7150000.0 ;   CAH  CAG
   5   6   2    0.153   7150000.0    0.153   7150000.0 ;   CAG  CAF
   6   7   2    0.153   7150000.0    0.153   7150000.0 ;   CAF  CAE
   7   8   2    0.153   7150000.0    0.153   7150000.0 ;   CAE  CAD
   8   9   2    0.153   7150000.0    0.153   7150000.0 ;   CAD  CAA

[ pairs ]
; ai  aj  fu    c0, c1, ...
   1   5   1                                           ;   OAB  CAG
   2   6   1                                           ;   CAI  CAF
   3   5   1                                           ;   OAC  CAG
   4   7   1                                           ;   CAH  CAE
   5   8   1                                           ;   CAG  CAD
   6   9   1                                           ;   CAF  CAA

[ angles ]
; ai  aj  ak  fu    c0, c1, ...
   1   2   3   2    126.0       770.0    126.0       770.0 ;   OAB  CAI
OAC
   1   2   4   2    117.0       635.0    117.0       635.0 ;   OAB  CAI
CAH
   3   2   4   2    117.0       635.0    117.0       635.0 ;   OAC  CAI
CAH
   2   4   5   2    109.5       520.0    109.5       520.0 ;   CAI  CAH
CAG
   4   5   6   2    109.5       520.0    109.5       520.0 ;   CAH  CAG
CAF
   5   6   7   2    109.5       520.0    109.5       520.0 ;   CAG  CAF
CAE
   6   7   8   2    109.5       520.0    109.5       520.0 ;   CAF  CAE
CAD
   7   8   9   2    109.5       520.0    109.5       520.0 ;   CAE  CAD
CAA

[ dihedrals ]
; ai  aj  ak  al  fu    c0, c1, m, ...
   2   1   3   4   2      0.0  167.4        0.0  167.4   ; imp   CAI  OAB
OAC  CAH
   5   4   2   1   1      0.0    1.0 6      0.0    1.0 6 ; dih   CAG  CAH
CAI  OAB
   6   5   4   2   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAF  CAG
CAH  CAI
   7   6   5   4   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAE  CAF
CAG  CAH
   8   7   6   5   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAD  CAE
CAF  CAG
   9   8   7   6   1      0.0    5.9 3      0.0    5.9 3 ; dih   CAA  CAD
CAE  CAF


Please help me to correct this mistake.
Many thanks.

Best regards,



Nguyen Van Cuong
PhD student - Curtin University of Technology
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