# Cannot add non-natural residues in charmm36 forcefield

**URL:** <https://gromacs.bioexcel.eu/t/cannot-add-non-natural-residues-in-charmm36-forcefield/1372>\
**Category:** User discussions\
**Created:** [January 2, 2021, 1:35pm UTC](https://gromacs.bioexcel.eu/t/cannot-add-non-natural-residues-in-charmm36-forcefield/1372 "2021-01-02T13:35:50Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![yiwenli](https://avatars.discourse-cdn.com/v4/letter/y/ecae2f/32.png) [@yiwenli](https://gromacs.bioexcel.eu/u/yiwenli)\
**Post date:** [January 2, 2021, 1:35pm UTC](https://gromacs.bioexcel.eu/t/cannot-add-non-natural-residues-in-charmm36-forcefield/1372/1 "2021-01-02T13:35:50Z")

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GROMACS version: gmx, 2020.4-MODIFIED  
GROMACS modification: Yes

I tried to add non-standard residues in gromacs. I updated residuetypes.dat, generated the topology file with the non-natural residue and the two adjacent residues as a whole, modified the rtp and hdb file for the new residue. I have successfully used this method to add unnatural amino acids in amber99 forcefield. But when I used the same method in charmm36 forcefield, it feedback a lot errors:  
ERROR2 [file topol. top, line 12284]: No default Bond types;  
ERROR3 [file topol. top, line 49986]: No default U-B types;  
ERROR30 [file topol. top, line 69670]: No default proper Dih. types;  
Fatal error: Unknown cmap torsion between atoms 1526 1528 1530

Are there any noteworthy differences in the way unnatural residues are handled in amber and charmm force fields?

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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, 2021, 3:48pm UTC](https://gromacs.bioexcel.eu/t/cannot-add-non-natural-residues-in-charmm36-forcefield/1372/2 "2021-01-05T15:48:47Z")

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It appears you have bonds between atom types that are not yet in the force field, so you need to add suitable parameters in ffbonded.itp and/or cmap.itp for the topology to be generated.

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**Author:** ![s.pallav](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/s.pallav/32/1099_2.png) [@s.pallav](https://gromacs.bioexcel.eu/u/s.pallav)\
**Post date:** [August 4, 2021, 2:44pm UTC](https://gromacs.bioexcel.eu/t/cannot-add-non-natural-residues-in-charmm36-forcefield/1372/3 "2021-08-04T14:44:51Z")

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How did you go about solving it? Will be helpful if you could share.

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**Author:** ![Nupur\_Nagar](https://avatars.discourse-cdn.com/v4/letter/n/858c86/32.png) [@Nupur\_Nagar](https://gromacs.bioexcel.eu/u/Nupur_Nagar)\
**Post date:** [August 6, 2021, 11:24am UTC](https://gromacs.bioexcel.eu/t/cannot-add-non-natural-residues-in-charmm36-forcefield/1372/4 "2021-08-06T11:24:30Z")

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Hi  
I generated the parameter file using Amber tools, added the parameters to ffbonded.itp and edited all the required files as suggested in following Gromacs tutorial:  
[https://manual.gromacs.org/documentation/current/how-to/topology.html](https://manual.gromacs.org/documentation/current/how-to/topology.html)