[gmx-users] g_x2top is missing bonds

Justin Lemkul jalemkul at vt.edu
Fri Feb 1 00:53:14 CET 2013

On 1/31/13 5:09 PM, FX wrote:
>> 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.
> I uploaded the files here: https://www.dropbox.com/s/w4ubappzljmkw35/gromacs.zip
> The thing is: if I take the example of ZN atoms, they are all equivalent by symmetry operations, so there's really only one type, and some of the ZN atoms are found by g_x2top.
> Things I have thought of so far:
>   -- It could possibly be some rounding issue, but I seems that the source code of g_x2top uses a 10% tolerance, which is more than enough for my system.
>   -- PBC issue? But some of the atoms near the cell boundaries are fine

Some are fine, others are way off.  The first two atoms g_x2top complains about 
are C3 and C5.  Turning on a periodic reference shows that C3 (missing two 
bonds) is 0.077 and 0.197 nm away from the two N atoms to which it should be 
bonded, far from the specified value of 0.130.  C5 (missing one bond) is 
similar, because one of the N atoms is 0.221 nm away, while the other N is fine 
at 0.126 nm.  I didn't check the rest, but I suspect the same issues apply.


>> 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 ;)
> Being involved in other open-source projects, I see very well what you mean.
> Thanks for your time,
> FX--
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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