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

Mark Abraham Mark.Abraham at anu.edu.au
Thu Nov 16 07:11:01 CET 2006

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. 

Yes, you'll probably have found some atom type info in the .atp file, 
but the "residue topology database" is in the .rtp file. pdb2gmx 
requires that all atoms belong to a residue in the .rtp file, and that 
the structure file names the residue correctly and the atoms in that 
residue in a manner consistent with the .rtp file. Thus at the very 
least, you'll need to create a residue for the iron in the .rtp file. 
Then you'll need to copy specbond.dat to your working directory, and 
edit it to add the bonds to the iron.

>On trying to get the top file from the DUNDEE 
> PRODRG server ,I faced the error as too many atoms in this molecule.It 
> will be more worthful if i come to know how to tackle this problem  or 
> possible way to obtain the .top file information in any other specific 
> databases.

In general, nobody has done your problem before, so you have to do it 
yourself. As far as I'm aware, the only automated tool is PRODRG and 
that has its limitations.


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