[gmx-users] importing RNA

Ken Rotondi ksr at chemistry.umass.edu
Thu Jan 6 18:09:41 CET 2005

I tried using pdb2gmx to import a pdb file with both protein and RNA in 
it. It failed with the error " Residue 'U' not found in residue 
topology database". I looked in the ffG43a2.rtp file and found that the 
gromacs names were ADE, GUA, CYT, and URA while my .pdb file had the 
names A, G, C, and U. I changed the ribonucleic acid names in the .itp 
file to reflect the names in the .pdb file and re-ran pdb2gmx, only to 
get the same error.
This seems like it should be simple, what am I missing?



K.S. Rotondi
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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