diff --git a/runpsipred b/runpsipred
index 4ccf44e..34dee99 100755
--- a/runpsipred
+++ b/runpsipred
@@ -14,13 +14,13 @@
 set dbname = uniref90filt
 
 # Where the NCBI programs have been installed
-set ncbidir = /usr/local/bin
+set ncbidir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
 
 # Where the PSIPRED V2 programs have been installed
-set execdir = ./bin
+set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
 
 # Where the PSIPRED V2 data files have been installed
-set datadir = ./data
+set datadir = @GENTOO_PORTAGE_EPREFIX@/usr/share/psipred/data
 
 set basename = $1:r
 set rootname = $basename:t
diff --git a/runpsipred_single b/runpsipred_single
index 1f7680b..7bd5bc3 100755
--- a/runpsipred_single
+++ b/runpsipred_single
@@ -10,10 +10,10 @@
 # NOTE: Script modified to be more cluster friendly (DTJ April 2008)
 
 # Where the PSIPRED V3 programs have been installed
-set execdir = ./bin
+set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
 
 # Where the PSIPRED V3 data files have been installed
-set datadir = ./data
+set datadir = @GENTOO_PORTAGE_EPREFIX@/usr/share/psipred/data
 
 set basename = $1:r
 set rootname = $basename:t