[gmx-users] A likely problem with ffgmx2.rtp

[Ivano Eberini]

Dear all,
while I was trying to understand the score for my dihedral problem, I 
realized a probelm with the GROMACS ff, specifically in the ffgmx2.rtp 
file (GLUH topology). The beta carbon seems to have too many bonds (5). 
The bond tagged with *** should be CA C and not CB C. Impropers seems to 
be OK. I hope I am not mistaken.

Best regards,
Ivano

[ GLUH ]
  [ atoms ]
      N     N  -0.280     0
      H     H   0.280     0
     CA    C1   0.000     1
     HA    HC   0.000     1
     CB    C2   0.000     2
    HB1    HC   0.000     2
    HB2    HC   0.000     2
     CG    C2   0.000     3
    HG1    HC   0.000     3
    HG2    HC   0.000     3
     CD     C   0.530     4
    OE1     O  -0.380     4
    OE2    OA  -0.548     4
    HE2    HO   0.398     4
      C     C   0.380     5
      O     O  -0.380     5
  [ bonds ]
      N     H
      N    CA
     CA    HA
     CA    CB		(1)
     CB     C			(2)***
     CB   HB1		(3)
     CB   HB2		(4)
     CB    CG		(5)
     CG   HG1
     CG   HG2
     CG    CD
     CD   OE1
     CD   OE2
    OE2   HE2
      C     O
     -C     N
  [ impropers ]
      N    -C    CA     H
     CA     N     C    CB
     CD   OE1   OE2    CG
     -C   -CA     N    -O