Best parameterization tool for novel molecules

User discussions
1

GROMACS version: version 2020.1-Ubuntu-2020.1-1
GROMACS modification: No

I’m currently trying to compute a energy minimization process using GROMACS and this tutorial.

I’ve created the molecule of interest by myself using Avogadro and produced a pdb file. This original pdb file should go thru parameterization for topology generation. I used swissparams, but unfortunately bumped into quite a bit of trouble. So I want to try another parameterization tool, hopefully an online one. Fyi, I’m using CHARMM27 force field. If you can reccomend me one, I would be really thankful.

Also I’m a novice user so if there is a mistake in my understanding, please feel free to correct me. Thanks!

2

Use http://cgenff.umaryland.edu/ to generate your ligand topology, and follow Protein-Ligand Complex

Use CHARMM36, not CHARMM27 (FYI there is no such protein force field, it is CHARMM22/CMAP), which has no ability to interface with CGenFF. The CHARMM36 port (available from the MacKerell lab web site linked in the tutorial I suggested) has full compatibility and all necessary atom types.