# Charge of modified lysines after refinement run

**URL:** <https://ask.bioexcel.eu/t/charge-of-modified-lysines-after-refinement-run/5917>\
**Category:** HADDOCK\
**Created:** [October 22, 2025, 2:51am UTC](https://ask.bioexcel.eu/t/charge-of-modified-lysines-after-refinement-run/5917 "2025-10-22T02:51:00Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![ef25](https://avatars.discourse-cdn.com/v4/letter/e/b38774/32.png) [@ef25](https://ask.bioexcel.eu/u/ef25)\
**Post date:** [October 22, 2025, 2:51am UTC](https://ask.bioexcel.eu/t/charge-of-modified-lysines-after-refinement-run/5917/1 "2025-10-22T02:51:00Z")

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Hello! I ran my WT protein in HADOOCK2.4 and wants to know the effect of modifying the lysines into different methylation status in the complex structure. So, after docking the WT, I changed the names of the LYS in my pdb to MLZ or MLY and ran the refinement. However, after the refinement, I noticed that no charge was assigned for the modified lysines. Does this affect the refinement result and how do I fix it?

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**Author:** ![VGPReys](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/vgpreys/32/960_2.png) [@VGPReys](https://ask.bioexcel.eu/u/VGPReys)\
**Post date:** [October 25, 2025, 6:51am UTC](https://ask.bioexcel.eu/t/charge-of-modified-lysines-after-refinement-run/5917/2 "2025-10-25T06:51:04Z")

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Dear user,

Charges are not present in the PDB file themselves, but rather in the force-field that we used.

If you can observe the proper methylation state on your modified Lysines, they should be taken into account during the computation and therefore the related force-field parameters used accordingly.  
If that is the case, the results are probably correct.