# Phosphorylation in serine and threonine

**URL:** <https://gromacs.bioexcel.eu/t/phosphorylation-in-serine-and-threonine/5772>\
**Category:** User discussions\
**Created:** [February 10, 2023, 8:06am UTC](https://gromacs.bioexcel.eu/t/phosphorylation-in-serine-and-threonine/5772 "2023-02-10T08:06:55Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![dp18](https://avatars.discourse-cdn.com/v4/letter/d/839c29/32.png) [@dp18](https://gromacs.bioexcel.eu/u/dp18)\
**Post date:** [February 10, 2023, 8:06am UTC](https://gromacs.bioexcel.eu/t/phosphorylation-in-serine-and-threonine/5772/1 "2023-02-10T08:06:55Z")

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GROMACS version:  
GROMACS modification: Yes/No  
Here post your question  
I am new to GROMACS and is using the same for trajectory analysis. I have phosphoserine and phosphothreonine generated in charmm36 ff. While running pdb2gmx I am getting the error ‘Atom PL in residue THR 114 was not found in rtp entry THR with 14 atoms while sorting atoms’. I have edited the charmm .rtp, atomtypes.atp and residuetypes.dat to include corresponding atom types.

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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:** [February 10, 2023, 2:28pm UTC](https://gromacs.bioexcel.eu/t/phosphorylation-in-serine-and-threonine/5772/2 "2023-02-10T14:28:30Z")

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Atom names must match what is defined in the `.rtp` entry corresponding to that residue. Correct the atom names in your coordinate file.

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**Author:** ![Jonatas](https://avatars.discourse-cdn.com/v4/letter/j/82dd89/32.png) [@Jonatas](https://gromacs.bioexcel.eu/u/Jonatas)\
**Post date:** [October 10, 2024, 7:21pm UTC](https://gromacs.bioexcel.eu/t/phosphorylation-in-serine-and-threonine/5772/3 "2024-10-10T19:21:41Z")

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Hello,  
Were you successful? I am experiencing the same problem and am unable to continue. I am working with the SER184 residue to which I add an acyl donor to this residue.