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

Mark Abraham mark.j.abraham at gmail.com
Thu Dec 27 02:20:10 CET 2012

On Thu, Dec 27, 2012 at 12:32 AM, Gert Peters <gert.peters at ugent.be> 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<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.

AMBER parameterizes the terminal residues differently from the non-terminal
residues. See rna.rtp. That requires that the terminal residues have a
different residue name that pdb2gmx can match accordingly. With the
information we have, nobody can say why one of your input files works and
the other doesn't.


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