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,
Matt
On Thu, 31 Jan 2013 19:32:36 -0000, FX <fxcoud...@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
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University College London
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