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

[Qing Liu]

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 is same as the protein atom numbers. As a result, Gromacs can not distinguish the ligand atoms and protein atoms in the sections "distance_restraints" and "angle_restraints". I also try to merge the topology of protein and ligand into a single file, where the ligand atom numbers are renumbered to be consecutive from the last protein atom. But this also does not work.  Can you help me? Thank you!






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Best wishes, 

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Qing Liu

Fudan Univ.

E-mail: 15110700076 at fudan.edu.cn