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

Thomas Piggot t.piggot at soton.ac.uk
Sun Jun 3 16:02:04 CEST 2012


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 



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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