Hi,
You may also need to name your terminal DNA residues appropriately in
your pdb file, as for the AMBER force fields the terminal DNA residues
are named differently. Check out the dna.rtp file for these naming
conventions.
Cheers
Tom
On 03/06/12 14:50, Justin A. Lemkul wrote:
On 6/3/12 9:47 AM, ramaraju801 wrote:
HI, everyone
am working on a system consisting of protein-DNA complex,where an
protein
comes and binds to the DNA to form a complex. To produce an topology
file in
gromacs i gave the command " pdb2gmx -f XXX.pdb -o XXX.gro -p
XXX.top -ter
-ignh -ff amber99 " .
its creating the topology files of the protein but when its starts
creating
the topology file for the DNA seq its recognizing the starting and the
ending terminus residue. and then stops giving an error
"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."
i tried editing the .n.tdb and .c.tbd files by writing the terminal
residues
of DNA in those files but then its giving an error which says need an
directive before the residue must been and old file
Editing these files won't actually help, I don't think. The .n.tdb
and .c.tdb contain terminal replacement instructions for proteins.
For DNA, you should not need them. The error is more indicative of
missing atoms. Consult the .rtp entry for your terminal nucleotides -
you need to have all the atoms present and named as the force field
expects them to be. You can't have anything missing or anything extra.
Also, copying and pasting error messages directly from the terminal is
vastly more helpful than a description.
-Justin
--
Dr Thomas Piggot
University of Southampton, UK.
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