diff --git a/spack.yaml b/spack.yaml
index 4f60b56f167c129c368de90b05d7b2ad27d59604..ab828d5e13a1087726741d07378ef5aa9b43efa6 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -3,7 +3,6 @@ spack:
     - site-config/$SYSTEMNAME
   specs:
     # EBRAINS tools
-    - apbs@3.4.0
     - arbor@0.9.0 +python +mpi
     - biobb-analysis@4.0.1
     - biobb-chemistry@4.0.0
@@ -38,7 +37,6 @@ spack:
     - py-netpyne@1.0.5
     - py-neurom@3.2.2
     - py-neuror@1.6.4
-    - py-pdb2pqr@3.5.2
     - py-pynn@0.11.0 +mpi
     - py-pyunicore@0.15.0
     - py-quantities-scidash@0.12.4.3