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

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Nov 16 09:23:11 CET 2006

Hi E.Elavazhagan,

The residue database does know HEME, containing iron. It is likely
that the problem is that the Fe ion is listed as a separate residue.
Make it part of the HEME residue and run pdb2gmx again.

Hope it helps,


On 11/16/06, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> E.Elavazhagan wrote:
> > Hai,
> > I am having the trouble to obtain the topology file while attaching the
> > prosthetic group to the target protein.Heme ion is surrounded by the
> > three aminoacids HIS243,ASP185,HIS183 which all are within 3 A'
> > distance.While I am using the G43a1 force filed ,the error is obtained
> > as   "Residue 'FE' not found in residue topology database".On referring
> > the files FFG43a1,ions in
> > "C:\cygwin\usr\local\gromacs\share\gromacs\top" we found the presence of
> > FE with the mass details.

Tsjerk A. Wassenaar, Ph.D.
NMR, Utrecht University,
Padualaan 8,
3584 CH Utrecht, the Netherlands
P: +31-30-2539931
F: +31-30-2537623

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