# Running MD with a UNL residue name in the pdb file

**URL:** <https://gromacs.bioexcel.eu/t/running-md-with-a-unl-residue-name-in-the-pdb-file/12637>\
**Category:** User discussions\
**Created:** [September 12, 2025, 5:10pm UTC](https://gromacs.bioexcel.eu/t/running-md-with-a-unl-residue-name-in-the-pdb-file/12637 "2025-09-12T17:10:56Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![ryanm](https://avatars.discourse-cdn.com/v4/letter/r/85f322/32.png) [@ryanm](https://gromacs.bioexcel.eu/u/ryanm)\
**Post date:** [September 12, 2025, 5:10pm UTC](https://gromacs.bioexcel.eu/t/running-md-with-a-unl-residue-name-in-the-pdb-file/12637/1 "2025-09-12T17:10:56Z")

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GROMACS version: 2023.5  
GROMACS modification: No

Hello,

The residue name is list as UNL. After running the GROMACS command to generate the topology, which fails because UNL is not listed in the residue topology database. Is it possible to manipulate GROMACS to identify the UNL residue name and generate the topology file to proceed towards MD production?

Ryan Molitor

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**Author:** ![ryanm](https://avatars.discourse-cdn.com/v4/letter/r/85f322/32.png) [@ryanm](https://gromacs.bioexcel.eu/u/ryanm)\
**Post date:** [September 12, 2025, 5:15pm UTC](https://gromacs.bioexcel.eu/t/running-md-with-a-unl-residue-name-in-the-pdb-file/12637/2 "2025-09-12T17:15:08Z")

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I am using the charmm36-jul2022 force-field on a local cluster.

Ryan Molitor

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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 12, 2025, 5:54pm UTC](https://gromacs.bioexcel.eu/t/running-md-with-a-unl-residue-name-in-the-pdb-file/12637/3 "2025-09-12T17:54:01Z")

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If it is a constituent residue in the chain of a biomolecule, you need to parametrize and validate the species, then write an .rtp entry for `pdb2gmx` to understand how to include it. If it is a noncovalently bound species like a ligand, you still need to parametrize and validate it, but then you can simply `#include` its topology in the system .top file.

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**Author:** ![ryanm](https://avatars.discourse-cdn.com/v4/letter/r/85f322/32.png) [@ryanm](https://gromacs.bioexcel.eu/u/ryanm)\
**Post date:** [September 12, 2025, 8:31pm UTC](https://gromacs.bioexcel.eu/t/running-md-with-a-unl-residue-name-in-the-pdb-file/12637/4 "2025-09-12T20:31:52Z")

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Thanks. Is it possible to run GROMACS at high temperatures, like 1000K to 5000K?

ryanm

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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 13, 2025, 2:12am UTC](https://gromacs.bioexcel.eu/t/running-md-with-a-unl-residue-name-in-the-pdb-file/12637/5 "2025-09-13T02:12:30Z")

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With a sufficiently small time step, yes, but no biomolecular force field has ever been validated at that temperature. I know from toying around at 500 K that peptide bonds will isomerize at that temperature, so you’re bound to get some strange behavior, which may or may not be correct. But you’d be in the wilderness in terms of convincing anyone that the model is valid.

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<div class="post-metadata">

**Author:** ![ryanm](https://avatars.discourse-cdn.com/v4/letter/r/85f322/32.png) [@ryanm](https://gromacs.bioexcel.eu/u/ryanm)\
**Post date:** [September 14, 2025, 1:00pm UTC](https://gromacs.bioexcel.eu/t/running-md-with-a-unl-residue-name-in-the-pdb-file/12637/6 "2025-09-14T13:00:43Z")

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I see. Thank you.