[gmx-users] RNA problem

Ken Rotondi ksr at chemistry.umass.edu
Thu Jan 6 20:39:05 CET 2005

Hello all,

I posted this about three hours ago and have not seen in show on the 
list, so here it goes again...

I have a problem running pdb2gmx on a .pdb file that contains both RNA 
and protein. The command returned the following error, "Residue 'U' not 
found in residue topology database". I opened the ffG43a2.rtp file and 
the ribonucleotides were named ADE, GUA, CYT and URA, while they were 
named as A, G, C, and U in the .pdb file. I edited the .rtp file, 
changing the ribonucleotide names to those in the .pdb file. Rerunning 
pdb2gmx resulted in the same error.
Seems like this should be simple, however...

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

If there's a solution, why worry? If there's no solution, why worry?  
The Dali Lamma

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