[gmx-users] g_x2top is missing bonds

Matt Watkins ucapmw0 at ucl.ac.uk
Thu Jan 31 22:03:57 CET 2013

Hey FX,

out of interest (and I ask off list as it is probably not very politically  
correct) why do you want to use gromacs? I've found it to be a nightmare  
for other than proteins/trivial systems.

Hope things are well,


On Thu, 31 Jan 2013 19:32:36 -0000, FX <fxcoudert at gmail.com> 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).
> Sincerely,
> FX
> 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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Dr Matthew Watkins
Dept. of Physics and Astronomy
University College London
phone: +44 20 7679 3436

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