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

[Justin Lemkul]

On 9/19/12 8:31 AM, naga sundar wrote:
> Dear simone
>
>                     I think so u r using the same pr.mdp and md.mdp files
> what u created initially. So open  both the mdp files replace DRG with UNK
> and the try sure it will work out.
>

The error is from pdb2gmx, so .mdp alterations will have no effect.  This error 
is commonly encountered with a variety of generic residue names (UNK, LIG, DRG, 
MOL, etc).  pdb2gmx is not magic; it has limited support for any non-protein or 
non-nucleic acid residues.  Only a limited number of cofactors and molecules are 
built into individual force fields, thus leaving the task of parameterization 
and/or addition of species to a force field to the user.

-Justin

> On Tue, Sep 18, 2012 at 9:44 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> 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/Errors#Residue_%27XXX%27_not_found_in_residue_topology_database>
>>
>> http://www.gromacs.org/**Documentation/How-tos/**Parameterization<http://www.gromacs.org/Documentation/How-tos/Parameterization>
>>
>> http://www.gromacs.org/**Documentation/How-tos/Adding_**
>> a_Residue_to_a_Force_Field<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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==============================**==========
>>
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>
>
>

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

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

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