[gmx-users] setting distance restraints between atoms belonging to different residues (Alessandra Villa)

[Sadaf Rani]

Thank you, Alessandra, for your reply.

I have a confusion here that when I merge the topology I will have to
reindex ligand atoms. *e.g *I have ligand topology starting with atom
number 1 and bond terms, angles, dihedrals have all the connectivity
numbering from 1 to so on.  When I will change the index number in combined
topology; will it not affect these terms? Could you please explain a bit
more? I have attached a ligand file for reference.
Thanks in advance.

Sadaf