# Non-standard amino acid alchemical mutation - dihedrals error

**URL:** <https://gromacs.bioexcel.eu/t/non-standard-amino-acid-alchemical-mutation-dihedrals-error/10225>\
**Category:** User discussions\
**Tags:** pdb2gmx\
**Created:** [September 24, 2024, 5:58am UTC](https://gromacs.bioexcel.eu/t/non-standard-amino-acid-alchemical-mutation-dihedrals-error/10225 "2024-09-24T05:58:51Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Vignesh\_SR](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/vignesh_sr/32/2457_2.png) [@Vignesh\_SR](https://gromacs.bioexcel.eu/u/Vignesh_SR)\
**Post date:** [September 24, 2024, 5:58am UTC](https://gromacs.bioexcel.eu/t/non-standard-amino-acid-alchemical-mutation-dihedrals-error/10225/1 "2024-09-24T05:58:51Z")

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GROMACS version: 2023.2  
GROMACS modification: No

Dear All,  
I am working on amino acid alchemical mutations and I found an interesting opportunity to mutate Arginine to Homoarginine for my study. I made mutres.mtp and mutres.rtp for this mutation ([R2Z](https://drive.google.com/file/d/12ftCezkJJzNjr5j36oK7K9cGxDLJJdZg/view?usp=sharing)) , based on the available data. I performed pdb2gmx step, after mutate.py and I got the following error.

 ![Dihedral_Error](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/c/c590419c3e86ad856bc7e0711438c0e6adca75c4.png)

Analyzing the answers from forums [eg](https://gromacs.bioexcel.eu/t/residues-in-one-molecule-have-a-different-all-dihedrals-type-0-and-1/4213) and dihedrals from ffbonded.itp, I tried several ways of growing and annihilating, naming the atoms. If the problem is in connection of diminishing and growing arms, how to handle the mutres.rtp in better way?  
Kindly help me with this issue.

Thanks in advance.

Best Regards,  
SR.

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<div class="post-metadata">

**Author:** ![Vignesh\_SR](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/vignesh_sr/32/2457_2.png) [@Vignesh\_SR](https://gromacs.bioexcel.eu/u/Vignesh_SR)\
**Post date:** [September 25, 2024, 12:40pm UTC](https://gromacs.bioexcel.eu/t/non-standard-amino-acid-alchemical-mutation-dihedrals-error/10225/2 "2024-09-25T12:40:47Z")

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This issue is resolved, as rightly pointed out by V Gapsys Sir.

Solution: add the [bondedtypes] section to .rtp file