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

[Gert Peters]

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?

Thanks in advance,

Kind regards,
Gert