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

Justin Lemkul jalemkul at vt.edu
Tue Jun 5 13:52:30 CEST 2018

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 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!

Put an [intermolecular_interactions] directive at the very end of your 
.top and then use [distance_restraints] and [angle_restraints] 
directives under it. Use global atom numbers (from the coordinate file, 
not the per-moleculetype numbering) to specify the interactions.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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