diff --git AmberTools/src/sander/makedepend AmberTools/src/sander/makedepend
index 984fd83f26..e14cdd851d 100755
--- AmberTools/src/sander/makedepend
+++ AmberTools/src/sander/makedepend
@@ -72,6 +72,11 @@ $modulefile{"UtilitiesModule"} = "utilitiesmodule";
 $modulefile{"random"} = "random";
 $modulefile{"constants"} = "constants";
 $modulefile{"SANDER_API_MOD"} = "interface";
+# ignore these modules
+
+# There exist modules, for example, defined by the fortran standard.
+# Ignore these for dependencies
+$ignore{"intrinsic"}=$ignore{"ieee_arithmetic"}=$ignore{"quick_api_module"}=$ignore{"iso_c_binding"}=$ignore{"mpi"} = 1;
 
 foreach $file ( <*.F90> ){
 	next if $file =~ /^_/;
@@ -112,12 +117,12 @@ foreach $file ( <*.F90> ){
 			($head,$usee) = /( *use) +(\w*)/;
 #			printf STDERR "     usee: $usee; modulefile is $modulefile{$usee}\n";
             
-            next if $usee eq "mpi";
-			if( !defined $modulefile{$usee} ){
+			next if defined $ignore{$usee}; 
+			if( !defined $modulefile{$usee}){
 				printf STDERR "No file name associated with module $usee\n";
 				exit(1);
 			}
-			if( !defined $used{ $fileroot,$modulefile{$usee} } ){
+			if( !defined $used{ $fileroot,$modulefile{$usee}}){
 
 				#  remove any circular references:
 				next if $fileroot eq $modulefile{$usee};