How to build Ligand topology

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GROMACS version: 2025
GROMACS modification: No

Hello everyone,

I am new to molecular dynamics simulations and I would like to confirm whether my procedure for building a ligand topology is correct, and how to properly validate that the topology has been generated correctly.

My ligand is α-D-mannosylglycerate, and I intend to use the CHARMM36 force field.

The workflow I followed is:

I downloaded the ligand structure in .sdf format and converted it to .mol2 using Avogadro.

I uploaded the ligand to the CGenFF server, which provided the following files:

  • .str

  • .err

  • .cgenff.mol2

  • gmx.pdb

  • gmx.top

To convert the CHARMM files to GROMACS format, I used the CGenFF Python script:

python2 cgenff_charmm2gmx.py LIGX LIGX.cgenff.mol2 LIGX.str charmm36-jul2022.ff

This generated four files:

  • .itp

  • .prm

  • .top

  • ini.pdb

I then converted the coordinate file to GROMACS format using:

gmx editconf -f ini.pdb -o .gro

Any guidance would be greatly appreciated.

Thank you.

2

Seems like that should work fine, you could check by visualizing the resulting .gro file or opening with a text editor to see if all the expected atoms are present, and check the .top to see if it’s calling the correct files. I’m assuming you were following Protein-Ligand Complex , which should give you the correct result especially since it’s been recently updated

1 Like
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Thank you :) yes I checked my files, they are showing all atoms and coordinates correctly.