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
--
========================================
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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