[gmx-users] distance constraints

[Michal Kolinski]

Thank you for advice.  In my case I have receptor protein with a ligand inside the active site of the receptor.  

I need to constrain distance between one of the receptors atom and one of the ligands atom to 

force a proper orientation of the ligand during the simulation.  As I understand  I have to 

combine both topologies (for receptor and ligand) and then put it in a single *.tip file. 

 Is there a simple way to  rewrite/renumber all the atoms of the ligand?

Michal
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