[gmx-users] Residue 'UNK' not found in residue topology database
naga25sundar at gmail.com
Wed Sep 19 14:31:21 CEST 2012
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
> 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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