[gmx-users] g_x2top is missing bonds

Justin Lemkul jalemkul at vt.edu
Thu Jan 31 22:47:10 CET 2013

On 1/31/13 2:32 PM, FX wrote:
> Hello,
> I'm trying to prepare a MD of a hybrid organic-inorganic crystal, i.e. only one big molecule extending throughout space with PBC. I have prepared my .gro file from the PDB (and checked it with babel/vmd). I'm trying to generate the topology with g_x2top. I have:
>    - created a directory for my forcefield
>    - suitable atomname2type.n2t in there
>    - forcefield.itp file with my bonded forcefield parameters
> However, g_x2top complains about not finding the expected number of bonds:
>> g_x2top -f zif8.gro -o topol.top -ff myff -name test -pbc
>> Fatal error:
>> Could only find a forcefield type for 240 out of 276 atoms
> The weird part is: all zinc atoms should be equivalent, so there is no reason for some to have 2 or 3 bonds while the others have 4 (as expected). Given that the .gro file is correct (including PBC), where could the problem come from? And how to diagnose it further?
> Thanks in advance for any hint, and apologies if I've not given enough information (or too much).

It would be useful to see the .n2t file and the screen output about what's 
problematic.  g_x2top cannot identify suitable entries in the .n2t file for 36 
of your atoms, so some combination of atoms is not accounted for, either by 
omission in the .n2t file or from a configuration that doesn't allow for 
combinations to be matched.

> Sincerely,
> FX
> PS: I don't know what's the policy on this list, so in doubt I attach the directory with my files

Attachments to the list are not accepted due to problems in the past.  It's best 
to post a link from which any necessary files can be downloaded.  Occasionally 
snippets of files are appropriate, but often times omitted information can be 
important and you might not know it ;)



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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