[Question]: My molecule has two parts, A and B. I want to calculate the interaction between AB, but I don't want to consider the AB interaction within the same molecule. What should I do

[kkivg]

My Question is...

My molecule has two parts, A and B. I want to calculate the interaction between AB, but I don't want to consider the AB interaction within the same molecule. What should I do

[kkivg]

And they are all non-standard residues

[marioernestovaldes]

Sorry for the delay! could you please attach a pdb of your molecule? it seems this is one molecule with two interacting sites. Having non-standard residues shouldn't be a problem as long as you define the topology.