# Can't find a force field that will accept my .pdb file

**URL:** <https://gromacs.bioexcel.eu/t/cant-find-a-force-field-that-will-accept-my-pdb-file/695>\
**Category:** User discussions\
**Created:** [August 22, 2020, 10:54pm UTC](https://gromacs.bioexcel.eu/t/cant-find-a-force-field-that-will-accept-my-pdb-file/695 "2020-08-22T22:54:50Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![burkew21](https://avatars.discourse-cdn.com/v4/letter/b/87869e/32.png) [@burkew21](https://gromacs.bioexcel.eu/u/burkew21)\
**Post date:** [August 22, 2020, 10:54pm UTC](https://gromacs.bioexcel.eu/t/cant-find-a-force-field-that-will-accept-my-pdb-file/695/1 "2020-08-22T22:54:50Z")

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GROMACS version: 2018

Hi everybody. I’m very much a beginner with GROMACS and MD software in general, but I’m interested in using it to model some self-assembled monolayers for my research. In any case, after assembling my desired system in Avogadro, I converted it to a .pdb file and then put it into pdb2gmx only to find that when I selected my desired force field it threw me a “Residue ‘UND’ not found in residue topology database” error.

I looked this error up in the GROMACS 2018 documentation, and although I now have somewhat of an idea of why this happened, I’m not entirely sure how to fix it. I find this even more puzzling because my initial system and choice of force field (AMBER99SB-ILDN) is pretty much identical to the paper I’m basing my procedure off of, and it appears to have worked for them. I’m not entirely sure what I did wrong here.

Any help on this matter would be greatly appreciated.

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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:** [August 23, 2020, 12:36am UTC](https://gromacs.bioexcel.eu/t/cant-find-a-force-field-that-will-accept-my-pdb-file/695/2 "2020-08-23T00:36:54Z")

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`pdb2gmx` can only generate topologies for residues it knows, which are all found in the `.rtp` file(s) for your force field. If your species is not there, you’ll have to add it: [http://manual.gromacs.org/current/how-to/topology.html#adding-a-new-residue](http://manual.gromacs.org/current/how-to/topology.html#adding-a-new-residue)

If someone has already done simulations with this non-standard residue, save yourself some effort and ask them to provide the corresponding force field files.