Trying to perturb a torsion with multiple terms

User discussions
1

GROMACS version:gromacs-2025.2
GROMACS modification: No
Hi, I would like to run a FEP simulation of a peptide for which I want to annihilate a terminal amino acid. I am using CHARMM force field and several torsions that I need to perturb contain terms with different multiplicities. When running grompp I get the error:

Cannot automatically perturb a torsion with multiple terms to different
form.
Please specify perturbed parameters manually for this torsion in your
topology!

The error message seems to suggest that this can be solved if I add the parameters manually in the top file. But when I tried to add the perturbation for a dihedral with two terms:

1 5 7 9 9 0.0 6.6944 1 0.0 6.6944 1 180.0 10.46 2 180.0 10.46 2

I get the error:

Incorrect number of parameters in interaction - found 12, expected 3 or 6
for Proper Dih. (after the function type). The interaction was
‘1 5 7 9 9 0.000000 6.694400 1 0.000000 6.694400 1
180.000000 10.460000 2 180.000000 10.460000 2’.

Is there a different way to solve this problem?

Thanks

2

I found the solution and I will post it here. For the example above to copy the set of torsion atoms twice:

1 5 7 9 9 0.0 6.6944 1 0.0 6.6944 1

1 5 7 9 9 180.0 10.46 2 180.0 10.46 2