[gmx-users] Error in generating a gromacs structure file for Arginine

[Pandya, Akash]

Hi all,

I'm trying to run MD simulations with Arginine. I'm using the AMBER99SB-ILDN FF and I get this error:

There is a dangling bond at at least one of the terminal ends and the force
field does not provide terminal entries or files. Fix your terminal residues
so that they match the residue database (.rtp) entries, or provide terminal
database entries (.tdb).

I've tried to search the error but don't know what I have done wrong? I used the command below:

gmx pdb2gmx -f Arg.pdb -o Arg.gro -water tip3p

The Arg.pdb looks like this:

COMPND    Arginine
AUTHOR    GENERATED BY OPEN BABEL 2.3.90
ATOM      1  O   Arg A   1      -2.303  -1.954  -0.204  1.00  0.00           O
ATOM      2  OXT Arg A   1      -3.444  -0.531   1.147  1.00  0.00           O
ATOM      3  N   Arg A   1      -2.892   1.602  -0.334  1.00  0.00           N
ATOM      4  NE  Arg A   1       1.964  -0.236   0.050  1.00  0.00           N
ATOM      5  NH1 Arg A   1       3.918  -1.417  -0.350  1.00  0.00           N
ATOM      6  NH2 Arg A   1       4.137   0.763   0.281  1.00  0.00           N
ATOM      7  CB  Arg A   1      -0.770   0.493  -0.870  1.00  0.00           C
ATOM      8  CG  Arg A   1      -0.171   0.875   0.492  1.00  0.00           C
ATOM      9  CA  Arg A   1      -2.299   0.356  -0.813  1.00  0.00           C
ATOM     10  CD  Arg A   1       1.345   1.033   0.437  1.00  0.00           C
ATOM     11  C   Arg A   1      -2.746  -0.721   0.159  1.00  0.00           C
ATOM     12  CZ  Arg A   1       3.260  -0.263   0.006  1.00  0.00           C
ATOM     13  HB1 Arg A   1      -0.337  -0.454  -1.215  1.00  0.00           H
ATOM     14  HB2 Arg A   1      -0.499   1.254  -1.613  1.00  0.00           H
ATOM     15  HG1 Arg A   1      -0.595   1.821   0.847  1.00  0.00           H
ATOM     16  HG2 Arg A   1      -0.419   0.109   1.237  1.00  0.00           H
ATOM     17  HA  Arg A   1      -2.702   0.120  -1.804  1.00  0.00           H
ATOM     18  HD1 Arg A   1       1.601   1.820  -0.282  1.00  0.00           H
ATOM     19  HD2 Arg A   1       1.695   1.340   1.430  1.00  0.00           H
ATOM     20  H1  Arg A   1      -3.908   1.542  -0.388  1.00  0.00           H
ATOM     21  H2  Arg A   1      -2.621   2.369  -0.949  1.00  0.00           H
ATOM     22  H   Arg A   1      -2.603  -2.648   0.421  1.00  0.00           H
ATOM     23 HH11 Arg A   1       3.406  -2.261  -0.582  1.00  0.00           H
ATOM     24 HH12 Arg A   1       4.931  -1.459  -0.390  1.00  0.00           H
ATOM     25 HH21 Arg A   1       5.140   0.625   0.213  1.00  0.00           H
ATOM     26 HH22 Arg A   1       3.821   1.686   0.556  1.00  0.00           H

CONECT    1   11   22
CONECT    2   11
CONECT    3    9   20   21
CONECT    4   10   12
CONECT    5   12   23   24
CONECT    6   12   25   26
CONECT    7    8    9   13   14
CONECT    8    7   10   15   16
CONECT    9    3    7   11   17
CONECT   10    4    8   18   19
CONECT   11    1    2    9
CONECT   12    4    5    6
CONECT   13    7
CONECT   14    7
CONECT   15    8
CONECT   16    8
CONECT   17    9
CONECT   18   10
CONECT   19   10
CONECT   20    3
CONECT   21    3
CONECT   22    1
CONECT   23    5
CONECT   24    5
CONECT   25    6
CONECT   26    6
MASTER        0    0    0    0    0    0    0    0   26    0   26    0
END

Please advise me on how to solve this error.


Akash