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
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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry
303 Engel Hall
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