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

[Qinghua Liao]

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 topology. I never tried, but it might work.


All the best,
Qinghua


On 06/05/2018 09:50 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!
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> Best wishes,
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> Qing Liu
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> Fudan Univ.
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> E-mail: 15110700076 at fudan.edu.cn