From: Nikhil Maroli (scinikhil_at_gmail.com)
Date: Mon Aug 21 2017 - 12:33:07 CDT
You can use https://cgenff.paramchem.org/ to generate topology parameters.
Now if you wanted to use Charmm-gui for your protein-ligand complex follow
1. Create a *.pdb file for the protein-ligand system with unique atom names.
2. Create a *.mol2 file for the ligand and upload it to charmm-gui.
Remember the naming in both *.mol2 and *.pdb should be unique.
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