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 <jalem...@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> > > ==============================**========== > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Regards N.NagaSundaram -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists