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

SIMONE BROGI brogi32 at unisi.it
Tue Sep 18 18:42:08 CEST 2012

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???
Thanks in advance for answers



Brogi Simone M.Sc. Ph.D.
Department of Pharmaceutical and Applied Chemistry
European Research Centre for Drug Discovery and Development
University of Siena
Via Aldo Moro
53100 Siena, Italy
Phone:+39 0577 234366 e-mail: brogi32 at unisi.it  simonebrogi1976 at hotmail.com
web: http://www.bronaldo.it     http://www.natsyndrugs.org
blog: http://bronaldo.spaces.live.com/

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