Preprocessing error with CGenFF 5.0 topology: unsupported multiple CHARMM type-9 dihedral parameters

User discussions
1

Gromacs Version : 2022

Hello everyone,

I am trying to run an energy minimization for a molecule generated using CGenFF 5.0 and cgenff_charmm2gmx.py.

I am using GROMACS 2022 and the following command:

gmx grompp -f minim.mdp -c box2.gro -p 969516.top -o min.tpr -maxwarn 1

During preprocessing, I get the following fatal errors:

ERROR [file 969516.prm, line 54]:
Encountered a second block of parameters for dihedral type 9 for the same atoms,
with either different parameters and/or the first block has multiple lines.
This is not supported.

Similar errors appear for lines 55, 63, 64, 65, 77, and 78.

The problematic entries are multi-term CHARMM dihedrals, for example:

CG2DC1 CG2DC1 CG2R61 CG2R61  9  180.000000  3.138000  2
CG2DC1 CG2DC1 CG2R61 CG2R61  9    0.000000  0.794960  4

and:

OG2D3 CG2O5 CG321 CG2O5  9  0.000000  3.598240  2
OG2D3 CG2O5 CG321 CG2O5  9  0.000000  5.564720  3
OG2D3 CG2O5 CG321 CG2O5  9  0.000000  1.548080  4

As far as I understand, these are valid CHARMM multi-term proper dihedrals with different multiplicities.

The [ dihedraltypes ] section of 969516.prm was generated by CGenFF and I did not modify it.

The relevant versions are:

  • GROMACS: 2022
  • CGenFF: 5.0
  • Topology generated using: cgenff_charmm2gmx.py

My questions are:

  1. Is this a compatibility issue between CGenFF 5.0 generated topologies and GROMACS 2022?
  2. Is there a recommended way to convert these multi-term CHARMM dihedrals for GROMACS 2022?
  3. Would upgrading to a newer GROMACS version (e.g. 2024/2025) solve this issue?

I would appreciate any guidance on the correct way to handle CGenFF multi-term dihedral parameters without manually removing terms.

Thank you.

cgenff_charmm2gmx-python.txt (32.1 KB)

969516_prm.txt (5.3 KB)