[gmx-users] FATAL ERROR: Residue "LIG" not found in residue topology database.

[Ali Alizadeh]

Dear All usres:

I am trying to do a simple system that contains 4 molecules ethane and
MD run using GROMACS. I build my .pdb file by using Avogadro software
. Afterwards, I try to generate the topology and .gro file using
pdb2gmx program and it generates an error. I am using the 43a1 force
field.


COMPND    UNNAMED
AUTHOR    GENERATED BY OPEN BABEL 2.3.0
HETATM    1  C   LIG     1      -1.328   5.677  -0.487  1.00  0.00           C
HETATM    2  C   LIG     1       0.160   5.696  -0.216  1.00  0.00           C
HETATM    3  C   LIG     2      -2.612   1.541  -0.437  1.00  0.00           C
HETATM    4  C   LIG     2      -1.247   1.959   0.060  1.00  0.00           C
HETATM    5  C   LIG     3      -0.924  -2.018   0.494  1.00  0.00           C
HETATM    6  C   LIG     3       0.583  -1.901   0.467  1.00  0.00           C
HETATM    7  C   LIG     4       0.836  -5.626  -0.170  1.00  0.00           C
HETATM    8  C   LIG     4       2.339  -5.464  -0.149  1.00  0.00           C
HETATM    9  H   LIG     1      -1.676   6.669  -0.790  1.00  0.00           H
HETATM   10  H   LIG     1      -1.878   5.379   0.410  1.00  0.00           H
HETATM   11  H   LIG     1      -1.564   4.970  -1.287  1.00  0.00           H
HETATM   12  H   LIG     1       0.396   6.406   0.582  1.00  0.00           H
HETATM   13  H   LIG     1       0.710   5.990  -1.115  1.00  0.00           H
HETATM   14  H   LIG     1       0.508   4.705   0.091  1.00  0.00           H
HETATM   15  H   LIG     2      -3.153   2.402  -0.840  1.00  0.00           H
HETATM   16  H   LIG     2      -3.203   1.113   0.378  1.00  0.00           H
HETATM   17  H   LIG     2      -2.520   0.790  -1.227  1.00  0.00           H
HETATM   18  H   LIG     2      -0.651   2.374  -0.758  1.00  0.00           H
HETATM   19  H   LIG     2      -0.709   1.102   0.476  1.00  0.00           H
HETATM   20  H   LIG     2      -1.338   2.717   0.843  1.00  0.00           H
HETATM   21  H   LIG     3      -1.230  -3.068   0.452  1.00  0.00           H
HETATM   22  H   LIG     3      -1.365  -1.498  -0.362  1.00  0.00           H
HETATM   23  H   LIG     3      -1.328  -1.578   1.410  1.00  0.00           H
HETATM   24  H   LIG     3       0.891  -0.853   0.527  1.00  0.00           H
HETATM   25  H   LIG     3       0.984  -2.323  -0.459  1.00  0.00           H
HETATM   26  H   LIG     3       1.025  -2.438   1.312  1.00  0.00           H
HETATM   27  H   LIG     4       2.612  -4.409  -0.060  1.00  0.00           H
HETATM   28  H   LIG     4       2.771  -6.003   0.699  1.00  0.00           H
HETATM   29  H   LIG     4       2.781  -5.858  -1.069  1.00  0.00           H
HETATM   30  H   LIG     4       0.564  -6.681  -0.264  1.00  0.00           H
HETATM   31  H   LIG     4       0.394  -5.238   0.753  1.00  0.00           H
HETATM   32  H   LIG     4       0.402  -5.082  -1.015  1.00  0.00           H
END


FATAL ERROR: Residue "LIG" not found in residue topology database.

Sincerely