[gmx-users] Dangling bond at terminal end of RNA rosetta model

Justin Lemkul jalemkul at vt.edu
Thu Dec 27 02:14:32 CET 2012

On 12/26/12 6:32 PM, Gert Peters wrote:
> Hi everybody,
> Im trying to use GROMACS for MD of a RNA model generated by Rosetta (FARFAR).
> As a test I try processing a modelledpdb file. When I prepare thetopology
> files (pdb2gmx -f test.pdb -ff amber99 -ignh ) from pdb I encounter following
> output :
> Sorting it all out... Opening force field file
> /usr/local/gromacs/share/gromacs/top/amber99.ff/aminoacids.hdb Opening force
> field file /usr/local/gromacs/share/gromacs/top/amber99.ff/dna.hdb Opening
> force field file /usr/local/gromacs/share/gromacs/top/amber99.ff/rna.hdb
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/amber99.ff/aminoacids.n.tdb Opening
> force field file
> /usr/local/gromacs/share/gromacs/top/amber99.ff/aminoacids.c.tdb
> Back Off! I just backed up topol.top to ./#topol.top.12# Processing chain 1
> 'A' (165 atoms, 8 residues) Identified residue rG1 as a starting terminus.
> Identified residue rC8 as a ending terminus. 8 out of 8 lines of specbond.dat
> converted successfully
> ------------------------------------------------------- Program pdb2gmx,
> VERSION 4.5.5 Source code file: pdb2top.c, line: 1031
> Fatal error: There is a dangling bond at at least one of the terminal ends
> and the force field does not provide terminal entries or files. Edit a .n.tdb
> and/or .c.tdb file. For more information and tips for troubleshooting, please
> check the GROMACS website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> When processing the corresponding structure from the pdb database (2IXZ)all
> files are generated as expected. I tried to compare the de novo model with
> the experimentally determined one but I cant find the problem(all terminal
> residues seem to have the same amountof atoms when ignoring the hydrogen
> atoms). I dont have a clue where to look next.
> Anyone got a clueto solve this issue?

The most common issue is residue name.  Terminal nucleic acids are named, e.g., 
RG5 to indicate 5' terminus.  Similarly, RG is an internal residue and RG3 is a 
3' terminal residue.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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