[gmx-users] pdb2gmx "dangling bond" error when trying to make periodically connected DNA

Viveca Lindahl vivecalindahl at gmail.com
Tue Feb 6 11:32:38 CET 2018

Hi again,

It seems from previous posts that this type of system setup is of general
interest so I thought I'd share the solution(s).

I modified the tdb file for the 5' end, here for CHARMM27, by adding the
following to the end of dna.n.tdb

[ hack ]
[ replace ]
C5'     C5'     CN8B    12.011     -0.08

Then in pdb2gmx -ter I choose 'hack' as the 5' terminal end. This gives the
C5' atom in the pdb file atomtype CN8B with charge -08 (which is the same
type and charge it would get if it was a non-terminal residue). For the 3'
end I choose 'none'.

Honestly, I don't know why it works -- looks like there still are "dangling
bonds" at both ends. But it seems to do the trick. The output looks like
what I want and no fatal errors. I think I'm just lucky in evading the
fatal error somehow. Another way to accomplish the same thing is to
recompile gmx with the fatal errors commented out.


On Fri, Feb 2, 2018 at 5:21 PM, Viveca Lindahl <vivecalindahl at gmail.com>

> Hi,
> I'm trying to create a topology for DNA with periodically connected ends.
> There's a previous message on this, with advice by Justin:
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_
> gmx-users/2015-April/096970.html
> I have a single-stranded DNA structure in a pdb file with a phosphate on
> one end (P, OP1, OP2) and an oxygen on the other (O3'). These are exactly
> the atoms I want to connect later on. I use pdb2gmx to get the hydrogens +
> topology and give it -ter "none", which gives me the error message
> "Fatal error:
> There is a dangling bond at at least one of the terminal ends. Fix your
> coordinate file, add a new terminal database entry (.tdb), or select the
> proper existing terminal entry."
> I added the flag -missing (according to Justin's advice), but does not
> help. I guess I'm not understanding what bond is dangling here, and what to
> add to the tdb file that would help?
> Of course, I could get most of the topology I need by avoiding selecting
> -ter 'none' but then I have to fiddle with adding back atoms.
> Best,
> Viveca

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