[gmx-users] Residue 'UNK' not found in residue topology database
jalemkul at vt.edu
Wed Sep 19 15:16:00 CEST 2012
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.
> 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
>> gmx-users mailing list gmx-users at gromacs.org
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Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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