# Topology creation for non-standard amino acid residues

**URL:** <https://gromacs.bioexcel.eu/t/topology-creation-for-non-standard-amino-acid-residues/10520>\
**Category:** User discussions\
**Created:** [November 11, 2024, 4:10pm UTC](https://gromacs.bioexcel.eu/t/topology-creation-for-non-standard-amino-acid-residues/10520 "2024-11-11T16:10:08Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Nik](https://avatars.discourse-cdn.com/v4/letter/n/6de8d8/32.png) [@Nik](https://gromacs.bioexcel.eu/u/Nik)\
**Post date:** [November 11, 2024, 4:10pm UTC](https://gromacs.bioexcel.eu/t/topology-creation-for-non-standard-amino-acid-residues/10520/1 "2024-11-11T16:10:08Z")

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GROMACS version:  
GROMACS modification: 2023.3

Is there any way to create a topology for non-standard amino acid residues (acylated serine in my case)?  
Of course some tools like CGENFF may be useful for separate molecules, but in my case it is necessary to get topology for acylated amino acid that is a part of protein chain.

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**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [November 12, 2024, 7:09am UTC](https://gromacs.bioexcel.eu/t/topology-creation-for-non-standard-amino-acid-residues/10520/2 "2024-11-12T07:09:39Z")

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See, e.g., [How can I generate a topology for a peptide contain unnatural amino acids and a linker ?](https://gromacs.bioexcel.eu/t/how-can-i-generate-a-topology-for-a-peptide-contain-unnatural-amino-acids-and-a-linker/3445), [Modified Residue topology - Gromacs 2020](https://gromacs.bioexcel.eu/t/modified-residue-topology-gromacs-2020/929) and [Topology creation for an acylated amino acid in Charmm force field](https://gromacs.bioexcel.eu/t/topology-creation-for-an-acylated-amino-acid-in-charmm-force-field/9962).