How to use ligand parameter file generated by ffTK in GROMACS?

User discussions
1

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!

2

You need to create new topology with optimised paramters you obtained after using the fftk.

3

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?

4

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?

5

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.

This isn’t about any particular molecule. Just a general question.

6

latest parameter file is the one you have updated with optimised paramters