# Generation of topology for non-standard molecules

**URL:** <https://gromacs.bioexcel.eu/t/generation-of-topology-for-non-standard-molecules/2789>\
**Category:** User discussions\
**Tags:** forcefield\
**Created:** [September 9, 2021, 11:39am UTC](https://gromacs.bioexcel.eu/t/generation-of-topology-for-non-standard-molecules/2789 "2021-09-09T11:39:15Z")\
**Posts on this page:** 4\
**Page:** 2

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [September 16, 2021, 1:13pm UTC](https://gromacs.bioexcel.eu/t/generation-of-topology-for-non-standard-molecules/2789/21 "2021-09-16T13:13:05Z")

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> [@Gourav](#):
>
> So let me get this straight, all I have to do is add my atom name and the corresponding atom types, followed by their charge, masses and connectivities (in terms of bond lengths) and I am good to go. Is that right?

Correct.

> [@Gourav](#):
>
> And if I have certain atoms which are not connected to other atoms the way I mentioned it, then it will throw an error. Is that right?

Correct.

> [@Gourav](#):
>
> Then can it be possible that the terminal atoms which have their connectivities open (as they are connected to the atoms of the next box) might be leading to the problem that I am facing?

Periodic distances are considered by default, so if these are the atoms causing problems, it means your box size is incorrect (perhaps too large such that the distances are not recognized as satisfying the criteria specified in the `.n2t` file).

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**Author:** ![Gourav](https://avatars.discourse-cdn.com/v4/letter/g/278dde/32.png) [@Gourav](https://gromacs.bioexcel.eu/u/Gourav)\
**Post date:** [September 16, 2021, 4:57pm UTC](https://gromacs.bioexcel.eu/t/generation-of-topology-for-non-standard-molecules/2789/22 "2021-09-16T16:57:48Z")

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Thank you for the help… But I will one last question here. I am getting problem due to a certain portion of bond. For example, I have defined an atom name OB and its atom type is OA. When I am running the x2top command, half of these are creating problem. I have looked at their bond lengths using both avogadro and materials studio and filled them accordingly, but still facing some error. Why is that only half of them is creating problem. Like I have 8 OB atoms, of which 4 are creating a problem with no forcefield found.

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [September 20, 2021, 5:30pm UTC](https://gromacs.bioexcel.eu/t/generation-of-topology-for-non-standard-molecules/2789/23 "2021-09-20T17:30:36Z")

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There’s not much more I can add beyond the suggestion I have already made. You will need to look at those atoms and determine what their nearest neighbors are, including across boundaries.

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**Author:** ![keinerfan](https://avatars.discourse-cdn.com/v4/letter/k/e495f1/32.png) [@keinerfan](https://gromacs.bioexcel.eu/u/keinerfan)\
**Post date:** [November 12, 2023, 8:10am UTC](https://gromacs.bioexcel.eu/t/generation-of-topology-for-non-standard-molecules/2789/24 "2023-11-12T08:10:56Z")

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Hi  
Im having same problem with silica nanoparticles and dont know how to parametrize them and generate toplogy if you have overcome the issue could you please email me the the solution?  
[erfan.nasrollahy.1381@gmail.com](mailto:erfan.nasrollahy.1381@gmail.com)

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