[gmx-users] specbond recognised but not built

[Grange Hermitage]

Hi all,
 
I am using gromacs 3.3.3, and have a specbond definition:
CHU     C3      2       CHV     C4      2       0.2     CHU     CHV
This is recognised but not built:
7 out of 7 lines of specbond.dat converted successfully
Special Atom Distance matrix:
                    CHU5
                    C341
    CHV9    C472   0.134
N-terminus: NH3+
C-terminus: COO-
Now there are 13 residues with 123 atoms
Making bonds...
Opening library file /home/users/ghermitage/gromacs/3.3.3/top/aminoacids.dat
Number of bonds was 121, now 121
.top:
[ atoms ]
48        CH1      5    CHU     C3     24          0     13.019   ; qtot -1.008
83        CH1      9    CHV     C4     42          0     13.019   ; qtot -2.016
Indeed, the bond is not built. No bond connecting the two atoms appears in [ bonds ]
What to do?
Thanks.
From ffgmx.rtp:
[ CHU ] 
[ atoms ]
   O         O       -0.669   1   
   C         C        0.380   1 
   CA        CH1      0.169   1
   N         NL       0.681   1
   H         H        0.004   1
   CB        CH2      0.299   1
   OG        OA      -0.171   1
   C1        CH2      0..299   1
   C3        CH1      0.000   2
[ bonds ]
 C     O 
 CA    C   
 CA    N   
 CA    CB   
 N     H  
 CB    OG   
 C1    OG   
 C1    C3   

[ CHV ] 
[ atoms ]
   O         O      -0.669   1    
   C         C       0.380   1    
   CA        CH1     0.169   1     
   N         NL      0.681   1  
   H         H       0.004   1   
   CB        CH2     0.299   1   
   OG        OA     -0.171   1   
   C2        CH2     0.299   1  
   C4        CH1     0.000   2 
[ bonds ]
   C     O   
   CA    C   
   CA    N   
   CA    CB   
   N     H   
   CB    OG   
   C2    OG   
   C2    C4   


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