There is no direct way to do this in APBS. However, you can do it by generating multiple dielectric maps (one for the ligand and one for the protein) and merging them for use in a subsequent calculation.
I hope this helps,
Pacific Northwest National Laboratory
From: Steve Zhu [mailto:firstname.lastname@example.org]
Sent: Monday, November 04, 2013 2:39 PM
Subject: [apbs-users] Using different pdie for the protein and the ligand in the protein-ligand complex?
Dear APBS users/developers,
I am working on the PB calculations of a protein-ligand complex recently. I wonder if there is an easy way to implement different pdie for the protein and the ligand in the complex calculations, for example, pdie=6 for the protein and pdie=1 for the ligand. Thank you very much!