# Protein-Ligand Complex new ligand Parameters input into .str INQUIRY? **URL:** \ **Category:** User discussions\ **Created:** [May 13, 2025, 12:51pm UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-new-ligand-parameters-input-into-str-inquiry/12077 "2025-05-13T12:51:23Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![mjsubach](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/mjsubach/32/387_2.png) [@mjsubach](https://gromacs.bioexcel.eu/u/mjsubach)\ **Post date:** [May 13, 2025, 12:51pm UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-new-ligand-parameters-input-into-str-inquiry/12077/1 "2025-05-13T12:51:23Z")
Hello Gromacs Forum: I have generated new parameters for a ligand due to penalties, accordingly before executing the below command beneath the Generate the JZ4 Topology with CGenFF heading: python cgenff\_charmm2gmx.py JZ4 jz4\_fix.mol2 jz4.str charmm36-jul2022.ff I believe that via default the proper procedure is to firstly change the the penalized parameter values to the re-parameterized values correct? For example I would change the original charge value of 0.483 below from within the originally generated .str file: ATOM C7 CG2RC0 0.483 ! 34.554 6 C 3 4 6 1 5 1 to the reparamterized -0.906 below from within the ffTK generated .1psf file: 10 X 3032 14C C7 CG2RC0 -0.906 12.0107 0 Your affirmation would be great, thanks if you know:) ---
**Author:** ![Marius](https://avatars.discourse-cdn.com/v4/letter/m/ed655f/32.png) [@Marius](https://gromacs.bioexcel.eu/u/Marius)\ **Post date:** [May 14, 2025, 7:45am UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-new-ligand-parameters-input-into-str-inquiry/12077/2 "2025-05-14T07:45:50Z")
Hi @mjsubach, I would follow the same approach by first updating the `.str` file with the reparameterized values and then running `cgenff_charmm2gmx.py`. To verify the results, you could compare single-point energies on the same ligand configuration in GROMACS (using the output from `cgenff_charmm2gmx.py`) with those from CHARMM or NAMD (using the modified `.str` file). Best, Marius ---
**Author:** ![mjsubach](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/mjsubach/32/387_2.png) [@mjsubach](https://gromacs.bioexcel.eu/u/mjsubach)\ **Post date:** [May 14, 2025, 9:57am UTC](https://gromacs.bioexcel.eu/t/protein-ligand-complex-new-ligand-parameters-input-into-str-inquiry/12077/3 "2025-05-14T09:57:45Z")
> [@Marius](#): > > CHARMM Hello Marius thank you for your kind update/affirmation:).