[gmx-users] Re: dangling bond at at one of the terminal ends

Justin A. Lemkul jalemkul at vt.edu
Sun Jun 3 15:50:30 CEST 2012

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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