[gmx-users] g_x2top is missing bonds

FX fxcoudert at gmail.com
Thu Jan 31 23:09:41 CET 2013

> 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

> 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,

More information about the gromacs.org_gmx-users mailing list