[gmx-users] Atom N21 not found

Ken Rotondi ksr at chemistry.umass.edu
Thu Sep 29 23:36:38 CEST 2005

Hello all,

I'm trying to run pdb2gmx on a ribo-protein. I'm getting an extremely 
strange error:
Program pdb2gmx, VERSION 3.3_beta_20050202
Source code file: add_par.c, line: 221

Fatal error:
Atom N21 not found in rtp database in residue GUA, it looks a bit like 

The first nucleotide on the first chain is GUA and there is no N21 atom 
defined in it or anywhere else (we did a global search of the file) in 
the .pdb file.

What could be causing this error?

Thanks as always,


K.S. Rotondi Ph.D.
Research Fellow
The Gierasch Laboratory
Department of Biochemistry and Molecular Biology
University of Massachusetts-Amherst
Phone: 413-545-1250
Fax;      413-545-3291

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