What to do when I have multiple occupancies?

[mysecondnameisdanger]

It is frequent to have multiple rotamers/conformations/alternative locations for some residues in a pdb file.
If I upload my pdb with both conformers to the pdb2pqr/apbs web server, one gets removed (I guess you only keep the first conformer and delete all others?)...
WARNING:main.py:424:setup_molecule:Multiple occupancies found in ASP A 18. At least one of the instances is being ignored.

What if the occupancies are 50% for conformer A and 50% for conformer B? should not pdb2pqr take into account that both scenarios can occur? Where I can find documentation on this?

Thanks

[sobolevnrm]

Hello. I believe PDB2PQR just takes the first conformer right now -- it does not accommodate both conformations.