Re: [gmx-users] How to add distance and angle restraints in the topology file?

On 6/5/18 3:50 AM, Qing Liu wrote: Hello, everyone, I just used Gromacs-5.1.4 to run a MD with distance and angle restraints. These restraints are between a protein and a ligand. However, the ligand topology is included in the "ligand.itp", and its atom numbers begin from 1. This

Re: [gmx-users] How to add distance and angle restraints in the topology file?

Hello, I guess you should add your ligand.itp to aminoacids.rtp, and then use pdb2gmx to generate a combined topology file. After that, you can use distance or angle restraints between the protein and the ligand. Maybe you can try to parmed from Amber to combine your protein and ligand