[gmx-users] g_x2top is missing bonds

[Matt Watkins]

Oops. Well, I'd be interested in people's opinions and don't intend to  
hijack FX's thread.

I do use the code regularly and greatly appreciate all the effort that  
people have put into its development. But, particularly, the inability to  
easily mix buckingham and lennard-jones is awkward for easily mixing  
inorganic/organic systems.

Apologies again to those offended, and maybe it could be a useful  
discussion,

Matt

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
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at  
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists


-- 
Dr Matthew Watkins
Dept. of Physics and Astronomy
University College London
phone: +44 20 7679 3436