How to create topology for a ligand

User discussions
1

GROMACS version: 2018.3
GROMACS modification: No

I picked a binding site from Autodock simulation, and saved the ligand at that binding site as a PDB.
Then I added its content to a protein PDB file by copying and pasting. (i.e. I tried to create a PDB file for protein-ligand complex)

After that, I ran pdb2gmx, and I got error as follows:
Residue ‘LIG’ not found in residue topology database

It seems to be saying there is no data on the ligand in the forcefield.
How do I solve the problem? I think I will need a step-by-step help on it. I am using AMBER99SB-ILDN forcefield.

Thank you.

2

pdb2gmx isn’t magic. It can only build topologies for species it knows. You can learn more about this at http://manual.gromacs.org/current/user-guide/run-time-errors.html#residue-xxx-not-found-in-residue-topology-database

As for the actual setup, please consider the following tutorial:

http://www.mdtutorials.com/gmx/complex/index.html

While my tutorial uses CHARMM, the same principles apply for any force field you might work with. You need to generate the ligand topology separately, in a manner consistent with the protein force field you’ve chosen to use.