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

Gert Peters gert.peters at ugent.be
Thu Dec 27 00:32:02 CET 2012

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 
Opening force field file 
Opening force field file 
Opening force field file 
Opening force field file 

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,

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