# Charmm36 ff with PTM on GROMACS

**URL:** <https://gromacs.bioexcel.eu/t/charmm36-ff-with-ptm-on-gromacs/10933>\
**Category:** User discussions\
**Tags:** forcefield\
**Created:** [January 2, 2025, 9:23pm UTC](https://gromacs.bioexcel.eu/t/charmm36-ff-with-ptm-on-gromacs/10933 "2025-01-02T21:23:18Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![Reza\_moosavi\_71](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/reza_moosavi_71/32/4191_2.png) [@Reza\_moosavi\_71](https://gromacs.bioexcel.eu/u/Reza_moosavi_71)\
**Post date:** [January 2, 2025, 9:23pm UTC](https://gromacs.bioexcel.eu/t/charmm36-ff-with-ptm-on-gromacs/10933/1 "2025-01-02T21:23:18Z")

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Hi everyone!

I have a question about using charmm36 ff on gromacs. I copied the ff to my gromacs ff folder (opt) and I have been using it with no problem. Recently, I need to work with a protein containing non-standard residues, and others with glycosilation. I used CHARMM-GUI to apply those PTMs or non-standarad amino acids on my protein; However, when I use GROMACS and the same charmm36 ff, GROMACS shows me and error and says the CGU residue is not standard and it is not listed in residuetypes.dat file. I searched for this file and there is no such file in my charmm36.ff folder.

Does anybody know what can I do to fix this problem?

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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:** [January 3, 2025, 1:18pm UTC](https://gromacs.bioexcel.eu/t/charmm36-ff-with-ptm-on-gromacs/10933/2 "2025-01-03T13:18:23Z")

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You should not need to use `pdb2gmx` at all if you built the system with CHARMM-GUI; it provides all necessary GROMACS input files, including a topology.

Dealing with extensive PTMs is a major headache in GROMACS. It is much easier to handle these kinds of systems in CHARMM.

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**Author:** ![Reza\_moosavi\_71](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/reza_moosavi_71/32/4191_2.png) [@Reza\_moosavi\_71](https://gromacs.bioexcel.eu/u/Reza_moosavi_71)\
**Post date:** [January 3, 2025, 5:24pm UTC](https://gromacs.bioexcel.eu/t/charmm36-ff-with-ptm-on-gromacs/10933/3 "2025-01-03T17:24:10Z")

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Thanks a lot for your response! Is there any way to learn charmm? is there a tutorial for its basics?

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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:** [January 5, 2025, 4:02am UTC](https://gromacs.bioexcel.eu/t/charmm36-ff-with-ptm-on-gromacs/10933/4 "2025-01-05T04:02:17Z")

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None that are particularly great, and none that will teach you everything you need to set up a system like this. But you don’t need one. CHARMM-GUI does it for you. As you said, you set up the system with PTMs with CHARMM-GUi. That should be the end of it. The server gives you everything you need to run GROMACS.