# How to use ligand parameter file generated by ffTK in GROMACS? **URL:** \ **Category:** User discussions\ **Tags:** forcefield\ **Created:** [March 22, 2024, 5:56pm UTC](https://gromacs.bioexcel.eu/t/how-to-use-ligand-parameter-file-generated-by-fftk-in-gromacs/8679 "2024-03-22T17:56:51Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![FreaX\_997](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/freax_997/32/2031_2.png) [@FreaX\_997](https://gromacs.bioexcel.eu/u/FreaX_997)\ **Post date:** [March 22, 2024, 5:56pm UTC](https://gromacs.bioexcel.eu/t/how-to-use-ligand-parameter-file-generated-by-fftk-in-gromacs/8679/1 "2024-03-22T17:56:51Z")
GROMACS version: 2023 GROMACS modification: No OS: Ubuntu 22.10 Hello everyone! This is quite a general question and has not got anything to do with any specific ligand. Let’s say I’ve got a ligand which is a small organic molecule (\< 50 atoms and made up of only carbons, hydrogens and oxygens) for which CGenFF, unfortunately, generates a few parameters with quite high penalties (\> 50). I download the `.str` file and use the `cgenff_charmm2gmx.py` script to generate the `.itp` and `.prm` files for the ligands. I now take the `.prm` file and modify the problematic parameters using ffTK (and ORCA for the necessary QM calculations). 1. How do I use this modified `.prm` file in preparing the protein-ligand simulation? 2. Will including the modified `.prm` file with the original `.itp` file in the `topol.top` file cause any issues/problems? 3. What advice would you give to a beginner like me who has encountered a “high CGenFF penalties” situation with a ligand they want to study? I would be extremely grateful for any insights into this situation and any suggestions I get. Thank you! ---
**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\ **Post date:** [March 22, 2024, 9:29pm UTC](https://gromacs.bioexcel.eu/t/how-to-use-ligand-parameter-file-generated-by-fftk-in-gromacs/8679/2 "2024-03-22T21:29:35Z")
You need to create new topology with optimised paramters you obtained after using the fftk. ---
**Author:** ![FreaX\_997](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/freax_997/32/2031_2.png) [@FreaX\_997](https://gromacs.bioexcel.eu/u/FreaX_997)\ **Post date:** [March 23, 2024, 7:09am UTC](https://gromacs.bioexcel.eu/t/how-to-use-ligand-parameter-file-generated-by-fftk-in-gromacs/8679/3 "2024-03-23T07:09:39Z")
Hey! Thanks for the reply. Can you tell me how I can create the new topology file? Is there any software/tool I can use to do this? ---
**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\ **Post date:** [March 23, 2024, 9:46pm UTC](https://gromacs.bioexcel.eu/t/how-to-use-ligand-parameter-file-generated-by-fftk-in-gromacs/8679/4 "2024-03-23T21:46:19Z")
If you are having high penalty; first step i advise is to optimise the geometry at the MP2 level. If the penalty is still high you may need to optimise those paramters using FFTK from VMD. Later, use the latest paramter file for the simulation. Which molecule is this? ---
**Author:** ![FreaX\_997](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/freax_997/32/2031_2.png) [@FreaX\_997](https://gromacs.bioexcel.eu/u/FreaX_997)\ **Post date:** [March 24, 2024, 6:58am UTC](https://gromacs.bioexcel.eu/t/how-to-use-ligand-parameter-file-generated-by-fftk-in-gromacs/8679/5 "2024-03-24T06:58:41Z")
> [@scinikhil](#): > > use the latest parameter file for the simulation This is exactly where I’m getting stuck. I don’t know what steps I should follow to use the latest parameter files in my GROMACS simulation. > [@scinikhil](#): > > Which molecule is this? This isn’t about any particular molecule. Just a general question. ---
**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\ **Post date:** [March 25, 2024, 4:16pm UTC](https://gromacs.bioexcel.eu/t/how-to-use-ligand-parameter-file-generated-by-fftk-in-gromacs/8679/6 "2024-03-25T16:16:07Z")
latest parameter file is the one you have updated with optimised paramters ---
**Author:** ![fatemeh](https://avatars.discourse-cdn.com/v4/letter/f/9de053/32.png) [@fatemeh](https://gromacs.bioexcel.eu/u/fatemeh)\ **Post date:** [June 27, 2025, 6:00pm UTC](https://gromacs.bioexcel.eu/t/how-to-use-ligand-parameter-file-generated-by-fftk-in-gromacs/8679/7 "2025-06-27T18:00:44Z")
> [@FreaX\_997](#): > > hanks for the reply. > > Can you tell me how I can create the new topology file? Is there any software/tool I can use to do Hello, Could you please let me know how you solved your problem? Did you use charmm-gui to convert it to gromacs version? Best regards,