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

[Justin Lemkul]

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:

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

http://www.gromacs.org/Documentation/How-tos/Parameterization

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

-Justin

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

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

========================================