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

[Justin A. Lemkul]

cuong nguyen wrote:
> 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.

This mailing list is for Gromacs-specific questions.  For PRODRG-related issues, 
please start with their FAQ (your question is answered there):

http://davapc1.bioch.dundee.ac.uk/prodrg/prodrg_faq.html

-Justin

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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