[gmx-users] problem with RNA

John Kerrigan kerrigje at UMDNJ.EDU
Fri Jul 12 19:22:35 CEST 2002


I'm a bit of a newbie to GROMACS.  I've been working with proteins on
gromacs (version 3.1.1) with no problems.  Nucleic acids, ughh!  Different

After careful edit of my rna.pdb file, I processed it with pdb2gmx (selected
0 for the Gromacs forcefield) and received no complaints (no warnings).
Solvated the beast with genbox, no problems.  I tried to grompp it in
preparation for energy minimization and I get the following error:

WARNING 1 [file "prna.top", line #]:
 No default Angle types, using zeroes
WARNING 2 ... etc.

Tracing the line # in the *.top file, I find that grompp doesn't like the
uridine residues.  The atom types appear to be reasonable.

Any suggestions are greatly appreciated.  Thanks in advance.


John E. Kerrigan, Ph.D.
Information Services and Technology

Adjunct Associate Professor
Department of Pharmacology

Robert Wood Johnson Medical School
University of Medicine and Dentistry of NJ
675 Hoes Lane
Piscataway, NJ 08854

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