diff -Naur vmd-1.8.7/configure vmd-1.8.7.new/configure
--- vmd-1.8.7/configure	2009-08-01 03:19:34.000000000 -0400
+++ vmd-1.8.7.new/configure	2009-08-07 09:12:43.000000000 -0400
@@ -13,10 +13,10 @@
 $install_name = "vmd";
 
 # Directory where VMD startup script is installed, should be in users' paths.
-$install_bin_dir="/usr/local/bin";
+$install_bin_dir="gentoo-bindir";
 
 # Directory where VMD files and executables are installed
-$install_library_dir="/usr/local/lib/$install_name";
+$install_library_dir="gentoo-libdir/$install_name";
 
 
 # optionally override hard-coded defaults above with environment variables
@@ -128,29 +128,6 @@
 # Configure script code begins here
 ############################################################################
 
-## Test for existence of a properly compiled plugin tree
-if (!(-e "plugins")) {
-  print "\n";
-  print "VMD plugin directory not found.\n";
-  print "Please compile the VMD plugins and do 'make distrib' to copy them\n";
-  print "into a 'plugins' directory linked or located in this directory.\n";
-  print "Be sure your PLUGINDIR environment variable is set before running\n";
-  print "'make distrib' in the plugin build area.\n";
-  print "\n";
-  die "Halting configuration until VMD plugins are built.\n";
-} else {
-  if (!(-e "plugins/include/vmdplugin.h")) {
-    print "\n";
-    print "VMD plugin include files or directory not found.\n";
-    print "Please compile the VMD plugins and do 'make distrib' to copy them\n";
-    print "into a 'plugins' directory linked or located in this directory.\n";
-    print "Be sure your PLUGINDIR environment variable is set before running\n";
-    print "'make distrib' in the plugin build area.\n";
-    print "\n";
-    die "Halting configuration until VMD plugins are built.\n";
-  }
-} 
-
 #################### Parse command line options   ###########
 # list of allowed architectures
 @archlist=('IRIX6', 'IRIX6_64', 'FREEBSD', 'HPUX11', 'AIX4', 'AIX5', 'AIX5_64', 'AIX6_64', 'LINUX', 'LINUXALPHA', 'LINUXAMD64', 'LINUXIA64', 'LINUXPPC', 'LINUXPPC64', 'MACOSX', 'MACOSXX86', 'MACOSXX86_64', 'TRU64', 'SOLARIS2', 'SOLARIS2_64', 'SOLARISX86', 'SOLARISX86_64', 'WIN32', 'WIN64');
@@ -435,7 +412,7 @@
 
 ################ Plugin options
 #
-$plugin_dir	= "../plugins";
+$plugin_dir	= "gentoo-plugindir";
 $plugin_include = "-I$plugin_dir/include";
 $plugin_library = "";
 $plugin_libs    = "";
@@ -448,7 +425,7 @@
 @plugin_extra   = ();
 
 if ($config_staticplugin) {
-  $molfile_dir = "$plugin_dir/$config_arch/molfile";
+  $molfile_dir = "$plugin_dir/compile/lib_LINUX/molfile";
   $plugin_include .= " -I$molfile_dir";
   $plugin_library .= " -L$molfile_dir";
   $plugin_libs    .= " -lmolfile_plugin";
@@ -550,8 +527,8 @@
 ################ FLTK GUI
 $fltk_defines     = "-DVMDGUI -DVMDFLTK";
 $fltk_dir         = "$vmd_library_dir/fltk";
-$fltk_include     = "-I$fltk_dir/include";
-$fltk_library     = "-L$fltk_dir/$config_arch";
+$fltk_include     = "-Igentoo-fltk-include";
+$fltk_library     = "-Lgentoo-fltk-libs";
 $fltk_libs        = "-lfltk -lX11";
 #@fltk_cc          = ('forms_ui.c');
 @fltk_cu          = ();
@@ -612,8 +589,8 @@
 if ($config_tk) { $tcl_include .= " -I$stock_tk_include_dir"; }
 $tcl_library      = "-L$stock_tcl_library_dir";
 if ($config_tk) { $tcl_library .= " -L$stock_tk_library_dir"; }
-$tcl_libs         = "-ltcl8.5";  
-if ($config_tk) { $tcl_libs = "-ltk8.5 -lX11 " . $tcl_libs; }
+$tcl_libs         = "-ltcl";  
+if ($config_tk) { $tcl_libs = "-ltk -lX11 " . $tcl_libs; }
 
 @tcl_cc           = ();
 @tcl_cu           = ();
@@ -938,8 +915,8 @@
 #######################
 $netcdf_defines     = "";
 $netcdf_dir         = "$vmd_library_dir/netcdf";
-$netcdf_include     = "-I$netcdf_dir/include";
-$netcdf_library     = "-L$netcdf_dir/lib_$config_arch";
+$netcdf_include     = "-Igentoo-netcdf-include";
+$netcdf_library     = "-Lgentoo-netcdf-libs";
 $netcdf_libs        = "-lnetcdf";
 @netcdf_cc          = ();
 @netcdf_cu          = ();
@@ -1007,9 +984,9 @@
 $python_defines     = "-DVMDPYTHON";
 $python_dir         = "$vmd_library_dir/python";
 $numpy_dir          = "$vmd_library_dir/numpy";
-$python_include     = "-I$python_dir/lib_$config_arch/include/python2.5 -I$numpy_dir/lib_$config_arch/include -I$python_dir/lib_$config_arch/lib/python2.5/site-packages/numpy/core/include";
-$python_library     = "-L$python_dir/lib_$config_arch/lib/python2.5/config";
-$python_libs        = "-lpython2.5 -lpthread";
+$python_include     = "-Igentoo-python-include -Igentoo-numpy-include";
+$python_library     = "-Lgentoo-python-lib";
+$python_libs        = "-lgentoo-python-link -lpthread";
 @python_h           = ('PythonTextInterp.h',
                        'VMDTkinterMenu.h',
 		       'py_commands.h',
@@ -1621,8 +1598,8 @@
 
     # XFree 4.0 Direct Rendering Interface and GLX 
     $opengl_dir         = "/usr/X11R6";
-    $opengl_include     = "-I$opengl_dir/include";
-    $opengl_library     = "-L$opengl_dir/lib";
+    $opengl_include     = "-Igentoo-opengl-include";
+    $opengl_library     = "-Lgentoo-opengl-libs";
     $opengl_libs        = "-lGL -lGLU"; 
     # $opengl_libs      = "-L/usr/X11R6/lib -lGL -lGLU -lXext -lX11";
 
@@ -1650,15 +1627,15 @@
       $arch_lopts       .= "-i-static ";
     } else {
       # compling with GCC
-      $arch_cc          = "gcc";
-      $arch_ccpp        = "g++";
+      $arch_cc          = "gentoo-gcc";
+      $arch_ccpp        = "gentoo-g++";
       $arch_depend_flag = "-MM";
-      $arch_shld        = "g++ -shared";
+      $arch_shld        = "gentoo-g++ -shared";
       $arch_shlibname   = "so";
       $arch_shcppopts   = "-fPIC";
       $arch_shldopts    = "";
-      $arch_opt_flag    = "-m32 -fno-for-scope -Wno-deprecated -Wall -O3";
-      $arch_copts       = "-m32 -Wall -O3";
+      $arch_opt_flag    = "gentoo-cflags";
+      $arch_copts       = "gentoo-cflags";
 
       if ($config_static) {
         $arch_lopts       = "-static";