[gmx-users] [Fwd: problem with URA residue in ffgmx]

David van der Spoel spoel at xray.bmc.uu.se
Fri Aug 16 16:23:35 CEST 2002

-----Forwarded Message-----

From: John Kerrigan <kerrigje at UMDNJ.EDU>
To: lindahl at stanford.edu
Cc: spoel at xray.bmc.uu.se
Subject: problem with URA residue in ffgmx
Date: 16 Aug 2002 10:05:43 -0400

Erik and David-

Help, pretty please?  I am working on an RNA model using the Gromacs 87
force field (ffgmx.rtp).  I solvate the RNA and am cruising along fine until
I grompp the system in preparation for energy minimization.  I have multiple
instances of the following error:

No default Angle types, using zeroes

When I trace the line numbers back, in every instance, the problem is with
the URA residue (uracil) and really makes no sense to me at all.  This was
written to file by pdb2gmx.  I had no hand in it.  Is it possible that the
default angle types for the uracil residue were inadverdantly left out of
the parameter set?  I checked the atom types for the angles in question and
they are consistent with atom types on other residues (like GUA and CYT) at
least for the ribose sugars.

grompp does not like the following four atom type combinations in URA.

OS  CS1  NR6*


NR6* CB  CR61

OA   CS1  CS1

I see this same error in versions 3.1.2 (windows) and 3.1.4 (unix).  Any

Thanks in advance for your help.


John E. Kerrigan, Ph.D.
Computational Biologist
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

(732) 235-4473  phone
(732) 235-5252  fax

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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