SAM co-factor with CHARMM force field for GROMACS silmualtion

User discussions
1

Hello All,

Following the GROMACS tutotial on Protein-ligand complex, I am trying to simulate a protein having SAM as one of its ligands using the CHARMM force field. All my attempts to get the topology file for SAM failed. I would like to know if anyone has succeeded in writing the topology (itp file for SAM with CHARMM FF) of this well-known ligand to help me do so as well.

Best,
Bourgeois

2

For CHARMM compatible topologies, I think your choices are CHARMM-GUI, https://cgenff.com/ or Brooks Lab - Match - University of Michigan (possibly via STaGE, GROMACS / STaGE ยท GitLab). Have you tried all these alternatives?

3

I have tried CHARMM-GUI and CGenFF but could not figure it out.