[gmx-users] g_x2top is missing bonds

FX fxcoudert at gmail.com
Thu Jan 31 20:32:36 CET 2013


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).


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

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