[gmx-users] Help with generating Arginine topology for Amber FF

[Pandya, Akash]

Hi all,

I'm trying to generate topology for arginine. I use the following command:

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

I get the following error:

Fatal error:
In the chosen force field there is no residue type for 'ARG' as a standalone
(starting & ending) residue

Please can someone guide me on how to solve this issue?

This is my coordinate file:

ATOM      1  O   ARG A   1       3.163   0.755   1.217  1.00  0.00           O1-
ATOM      2  OXT ARG A   1       3.741   0.815  -0.992  1.00  0.00           O
ATOM      3  NE  ARG A   1      -2.229  -0.118  -0.364  1.00  0.00           N1+
ATOM      4  N   ARG A   1       2.680  -1.912   0.462  1.00  0.00           N
ATOM      5  NH1 ARG A   1      -4.417  -1.176  -0.271  1.00  0.00           N
ATOM      6  NH2 ARG A   1      -4.077   0.991   0.701  1.00  0.00           N
ATOM      7  CB  ARG A   1       0.686  -0.545   0.119  1.00  0.00           C
ATOM      8  CG  ARG A   1       0.099   0.711  -0.538  1.00  0.00           C
ATOM      9  CA  ARG A   1       2.142  -0.780  -0.295  1.00  0.00           C
ATOM     10  CD  ARG A   1      -1.326   0.993  -0.070  1.00  0.00           C
ATOM     11  C   ARG A   1       3.109   0.376   0.014  1.00  0.00           C
ATOM     12  CZ  ARG A   1      -3.572  -0.110   0.017  1.00  0.00           C
ATOM     13  HB1 ARG A   1       0.090  -1.427  -0.144  1.00  0.00           H
ATOM     14  HB2 ARG A   1       0.620  -0.431   1.210  1.00  0.00           H
ATOM     15  HG1 ARG A   1       0.715   1.588  -0.312  1.00  0.00           H
ATOM     16  HG2 ARG A   1       0.104   0.580  -1.627  1.00  0.00           H
ATOM     17  HA  ARG A   1       2.179  -1.018  -1.366  1.00  0.00           H
ATOM     18  HD1 ARG A   1      -1.699   1.886  -0.583  1.00  0.00           H
ATOM     19  HD2 ARG A   1      -1.323   1.163   1.012  1.00  0.00           H
ATOM     20  HE  ARG A   1      -1.895  -0.929  -0.880  1.00  0.00           H
ATOM     21  H1  ARG A   1       3.603  -2.156   0.104  1.00  0.00           H
ATOM     22  H2  ARG A   1       2.095  -2.733   0.313  1.00  0.00           H
ATOM     23 HH11 ARG A   1      -4.078  -1.995  -0.770  1.00  0.00           H
ATOM     24 HH12 ARG A   1      -5.395  -1.165   0.009  1.00  0.00           H
ATOM     25 HH21 ARG A   1      -3.505   1.798   0.934  1.00  0.00           H
ATOM     26 HH22 ARG A   1      -5.052   1.019   0.990  1.00  0.00           H
CONECT    1   11
CONECT    2   11
CONECT    3   10   12   20
CONECT    4    9   21   22
CONECT    5   12   23   24
CONECT    6   12   25   26
CONECT    7    8    9   13   14
CONECT    8    7   10   15   16
CONECT    9    4    7   11   17
CONECT   10    3    8   18   19
CONECT   11    1    2    9
CONECT   12    3    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    4
CONECT   22    4
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

Thanks,

Akash