I am trying to use multiple PDB files using the PMI multiscale modelling
protocol. I'm doing it by creating different PMI.states within the main
system. Is this the IMP.pmi way to do it?
What are you trying to achieve here? Multistate modeling is used when
you have multiple conformations and/or compositions present in your
sample, such that your experimental data can only be satisfied by
multiple models (e.g. closed/open form, see https://salilab.org/phoq for
an example).
You can, of course, use multiple PDB files as input for regular
single-state modeling (a typical application would use a separate PDB
file for each subunit in a complex). Just list them all in your topology
file or Python script.