[gmx-users] 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.

[Mark Abraham]

On 31/05/2012 4:13 PM, ramaraju801 wrote:
> when i ran gromacs to produce topology file for a nucleotide sequence it is
> showing the above error saying  "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".

... or maybe you need to use pdb2gmx correctly. Since you haven't told 
us how you've used it, we can't help. Make sure you've done any 
DNA-protein tutorials you can find, and applied any lessons you may learn.

>    i tried giving the starting and
> ending residues in .n.tdb and .c.tdb files but it did not work  with an
> error saying "Fatal error:
> reading termini database: directive expected before line:
> P"

So you've broken the file format. Re-read the relevant part of chapter 5 
of the manual and try again.

Mark

> am uploading my PDB file of my DNA-protein compex sequence in which  the
> nucleotide sequence ranges from 15555 to 12216
> http://gromacs.5086.n6.nabble.com/file/n4997922/dnaseq_rot1.pdb
> dnaseq_rot1.pdb
>
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