[gmx-users] Reg pdb2gmx

Mark Abraham Mark.Abraham at anu.edu.au
Thu Oct 19 06:55:36 CEST 2006

Sivashangari Gnanasambandam wrote:
> Dear all,
>  I am novoice to gromacs. I had created a pdb file using Material studio 
> Modelling. Whe I use this file to convert to top ology file it shows an 
> error that the
> Error message - Residue 'rea' not found in residue topology database.
> I had attached the pbf file created. I was struggling to figure out the 
> solution for the past one week. Plz kindly help me to solve this problem.

PDB file format description here 

Columns 18-20 of a PDB file contain the residue name, but column 21 can 
sometimes be fudged to extend that. Your PDB file is using column 17 
inappropriately for that fudge, so pdb2gmx is reading "rea" for "urea". 
Presumably this means the software you created it with was written by 
someone who didn't understand file format descriptions. You should be 

To fix it, you should use columns 18-20 to contain whatever the name for 
urea is in the residue topology database (.rtp file) for the force field 
you're using.


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