[gmx-users] Residue 'UNK' not found in residue topology database

Justin Lemkul jalemkul at vt.edu
Tue Sep 18 18:44:00 CEST 2012

On 9/18/12 12:42 PM, SIMONE BROGI wrote:
> Dear gromacs user,
> I have a complex generated by docking calculation and I would perform a MD
> by gromacs. I have a problem with ligand atoms. In the pdb file the ligand
> appears as UNK and if I process this file in order to start simulation I
> receive this messagge error:
>   "Residue 'UNK' not found in residue topology database"
>   this part of file concerning ligand and it is not a residue. In order to
> fix this problem can I replace the UNK with another tag that is Known in
> topology database for a ligand??? or How can I fix this error???

Most ligands are not part of existing force fields.  Please consult the following:






Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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