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

[naga sundar]

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.

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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-- 
Regards
N.NagaSundaram