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

[Justin Lemkul]

On 7/31/12 7:48 AM, Ali Alizadeh wrote:
> 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.
>

pdb2gmx isn't magic:

http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database

-Justin

>
> 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
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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