# Wrong out put for gmx x2top?

**URL:** <https://gromacs.bioexcel.eu/t/wrong-out-put-for-gmx-x2top/9738>\
**Category:** User discussions\
**Created:** [July 25, 2024, 9:16am UTC](https://gromacs.bioexcel.eu/t/wrong-out-put-for-gmx-x2top/9738 "2024-07-25T09:16:16Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![mj.rezayani](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/mj.rezayani/32/3918_2.png) [@mj.rezayani](https://gromacs.bioexcel.eu/u/mj.rezayani)\
**Post date:** [July 25, 2024, 9:16am UTC](https://gromacs.bioexcel.eu/t/wrong-out-put-for-gmx-x2top/9738/1 "2024-07-25T09:16:16Z")

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Dear users,

I would like to simulate a zeolite structure in gromacs. I got the .cif file from IZA expanded in one direction in Materials Studio and exported a .pdb file. However, when I want to use gmx x2top to get the topology file I see that bonds and angles are not defined correctly. For example, it defines 8 bonds for oxygen atom. This bug was the main problem for segmentation error while running NVT and NPT. What should I do to address this issue? I also attached the pdb file here. I changed the file format to .txt because of website limitations.  
[MFI\_Z.txt](https://gromacs.bioexcel.eu/uploads/short-url/lq14qCTrFqljkmJA5FgPu4mYnFx.txt) (71.4 KB)

Thanks