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

--
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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