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

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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