diff --git a/GSM/bmat.cpp b/GSM/bmat.cpp
index 6957849..06d7719 100644
--- a/GSM/bmat.cpp
+++ b/GSM/bmat.cpp
@@ -347,7 +347,7 @@ int ICoord::bmatp_to_U()
   //    printf(" %8.5f",G[i1*len+j]);
   //  printf("\n");
 #endif
-    lowev++;
+//  lowev++;
   }
   if (lowev>0)
     printf(" lowev: %i",lowev);
diff --git a/GSM/icoord.cpp b/GSM/icoord.cpp
index 5e7cadd..2ca8976 100644
--- a/GSM/icoord.cpp
+++ b/GSM/icoord.cpp
@@ -175,7 +175,7 @@ void ICoord::create_xyz()
   return;
 }
 
-///creates the internal coordinates
+
 int ICoord::ic_create()
 {
   make_bonds();
@@ -286,31 +286,47 @@ void ICoord::hbond_frags()
           a3 = b2;
         if (b2==a1 && anumbers[b1]==1)
           a3 = b1;
-        water[3*nwater+0] = a1;
-        water[3*nwater+1] = a2;
-        water[3*nwater+2] = a3;
-        nwater++; 
-        break;
+        if (a3>-1)
+        {
+          water[3*nwater+0] = a1;
+          water[3*nwater+1] = a2;
+          water[3*nwater+2] = a3;
+          nwater++; 
+          break;
+        }
       } 
     } //loop j over nbonds
 
   } //loop i over oxygen atoms
 
-//  printf("  found %2i water molecules \n",nwater);
-//  for (int i=0;i<nwater;i++)
-//    printf("   OHH: %2i %2i %2i \n",water[3*i+0]+1,water[3*i+1]+1,water[3*i+2]+1);
+#if 0
+  for (int i=0;i<nwater;i++)
+  if (water[3*i+0]==-1 || water[3*i+1]==-1 || water[3*i+2]==-1)
+  {
+    printf("   removing water %i \n",i);
+    nwater--;
+  }
+#endif
+
+  printf("  found %2i water molecules \n",nwater);
+  for (int i=0;i<nwater;i++)
+    printf("   OHH: %2i %2i %2i \n",water[3*i+0]+1,water[3*i+1]+1,water[3*i+2]+1);
+
+  int* addw = new int[nwater];
+  for (int i=0;i<nwater;i++) addw[i] = 0;
 
   for (int i=0;i<nwater;i++)
   for (int j=0;j<nwater;j++)
   if (i!=j)
   {
-   // printf(" bond check on: %i %i \n",water[3*i+0],water[3*j+1]);
+//    printf(" bond check on: %i %i - %4.2f %4.2f \n",water[3*i+0],water[3*j+1],distance(water[3*i+0],water[3*j+1]),distance(water[3*i+0],water[3*j+2]));
     if (distance(water[3*i+0],water[3*j+1])<2.0 && !bond_exists(water[3*i+0],water[3*j+1]))
     {
       printf("   adding H-bond as bond: %i %i \n",water[3*i+0]+1,water[3*j+1]+1);
       bonds[nbonds][0] = water[3*i+0];
       bonds[nbonds][1] = water[3*j+1];
       nbonds++;
+      addw[i]++; addw[j]++;
     }
     if (distance(water[3*i+0],water[3*j+2])<2.0 && !bond_exists(water[3*i+0],water[3*j+2]))
     {
@@ -318,9 +334,44 @@ void ICoord::hbond_frags()
       bonds[nbonds][0] = water[3*i+0];
       bonds[nbonds][1] = water[3*j+2];
       nbonds++;
+      addw[i] = 1; addw[j]++;
     }
   }
 
+  printf("\n addw:");
+  for (int i=0;i<nwater;i++) 
+    printf(" %i",addw[i]);
+  printf("\n");
+
+  for (int i=0;i<nwater;i++)
+  if (addw[i]<2)
+  {
+    printf("   need water bond for %2i \n",i+1);
+    for (int j=0;j<nwater;j++)
+    if (i!=j)
+    {
+      if (distance(water[3*i+0],water[3*j+1])<3.0 && !bond_exists(water[3*i+0],water[3*j+1]))
+      {
+        printf("   adding H-bond as bond: %i %i \n",water[3*i+0]+1,water[3*j+1]+1);
+        bonds[nbonds][0] = water[3*i+0];
+        bonds[nbonds][1] = water[3*j+1];
+        nbonds++;
+        addw[i] = 1; addw[j]++;
+      }
+      if (distance(water[3*i+0],water[3*j+2])<3.0 && !bond_exists(water[3*i+0],water[3*j+2]))
+      {
+        printf("   adding H-bond as bond: %i %i \n",water[3*i+0]+1,water[3*j+2]+1);
+        bonds[nbonds][0] = water[3*i+0];
+        bonds[nbonds][1] = water[3*j+2];
+        nbonds++;
+        addw[i] = 1; addw[j]++;
+      }
+    }
+  }
+
+  delete [] addw;
+  delete [] water;
+
   return;
 }
 
@@ -854,6 +905,7 @@ void ICoord::bond_frags()
     b1 = -1;
     b2 = -1;
     mclose2 = 1000.;
+    if (a1>-1 && a2>-1)
     for (int i=0;i<natoms;i++)
     for (int j=0;j<natoms;j++)
     if (frags[i]==n1 && frags[j]==n2)
@@ -881,6 +933,8 @@ void ICoord::bond_frags()
     c1 = -1;
     c2 = -1;
     mclose3 = 1000.;
+    if (a1>-1 && a2>-1)
+    if (b1>-1 && b2>-1)
     for (int i=0;i<natoms;i++)
     for (int j=0;j<natoms;j++)
     if (frags[i]==n1 && frags[j]==n2)
@@ -1586,14 +1640,30 @@ double ICoord::getR(int i){
   else if (anumbers[i]==28) value = 3.0;
   else if (anumbers[i]==29) value = 3.0;
   else if (anumbers[i]==30) value = 3.0;
+	else if (anumbers[i]==31) value = 2.8;  //CRA guess
+	else if (anumbers[i]==32) value = 2.8;  //CRA guess
+	else if (anumbers[i]==33) value = 2.7;  //CRA scale based on 3rd row
+	else if (anumbers[i]==34) value = 2.55; //CRA scale based on 3rd row
   else if (anumbers[i]==35) value = 2.7;
+	else if (anumbers[i]==37) value = 4.0; //CRA same as  4th row
+	else if (anumbers[i]==38) value = 3.5; //CRA same as  4th row
+	else if (anumbers[i]==39) value = 4.5; //CRA same as  4th row
   else if (anumbers[i]==40) value = 3.35;
+	else if (anumbers[i]==41) value = 3.3; //CRA guess
+	else if (anumbers[i]==42) value = 3.3; //CRA guess
+	else if (anumbers[i]==43) value = 3.3; //CRA guess; radioactive
   else if (anumbers[i]==44) value = 3.2;
   else if (anumbers[i]==45) value = 3.15;
   else if (anumbers[i]==46) value = 3.15;
   else if (anumbers[i]==47) value = 3.25;
+	else if (anumbers[i]==48) value = 3.27; //CRA scale same as Zn
+	else if (anumbers[i]==49) value = 3.0;  //CRA guess
+	else if (anumbers[i]==50) value = 3.0;  //CRA guess
+	else if (anumbers[i]==51) value = 2.9;  //CRA guess
+	else if (anumbers[i]==52) value = 2.9;  //CRA guess
   else if (anumbers[i]==53) value = 2.8; //iodine
   else if (anumbers[i]==55) value = 4.2;
+	else if (anumbers[i]==72) value = 3.3; //CRA guess 
   else if (anumbers[i]==73) value = 3.3;
   else if (anumbers[i]==74) value = 3.3;
   else if (anumbers[i]==75) value = 3.3;
@@ -1601,9 +1671,14 @@ double ICoord::getR(int i){
   else if (anumbers[i]==77) value = 3.35;
   else if (anumbers[i]==78) value = 3.35;
   else if (anumbers[i]==79) value = 3.45;
+  else if (anumbers[i]==81) value = 3.25; //CRA guess
+  else if (anumbers[i]==82) value = 3.25; //CRA guess
+  else if (anumbers[i]==83) value = 3.25; //CRA guess
+  else if (anumbers[i]==84) value = 3.25; //CRA guess
+  else if (anumbers[i]==85) value = 3.25; //CRA guess
   else 
   {
-    printf(" Need to add atomic number %i to getR! \n",anumbers[i]);
+    printf(" Need to add atomic number %i (of atom %i) to getR! \n",anumbers[i],i+1);
     exit(1);
   }
 //  else value = 0.;
diff --git a/GSM/mopac.cpp b/GSM/mopac.cpp
index d183d9c..17ebe63 100644
--- a/GSM/mopac.cpp
+++ b/GSM/mopac.cpp
@@ -3,7 +3,8 @@ using namespace std;
 #include "constants.h"
 
 //#define MOPAC_LEVEL "PM6 NOSYM 1SCF GRADIENTS UHF TRIPLET CHARGE=1"
-#define MOPAC_LEVEL "PM6 NOSYM 1SCF GRADIENTS UHF AUX "
+//#define MOPAC_LEVEL "PM6-DH2 NOSYM 1SCF GRADIENTS UHF AUX "
+#define MOPAC_LEVEL "PM7 NOSYM 1SCF GRADIENTS UHF AUX "
 //#define MOPAC_LEVEL "PM6 NOSYM 1SCF GRADIENTS UHF AUX CHARGE=1 "
 
 void Mopac::write_ic_input(ofstream& inpfile, int anum, ICoord ic){
diff --git a/Makefile b/Makefile
index 0123b57..d2308ef 100644
--- a/Makefile
+++ b/Makefile
@@ -25,12 +25,12 @@ F95ROOT = $(MKLROOT)
 #LINKERFLAGS =  -L$(MKLROOT)/lib/em64t $(F95ROOT)/lib/em64t/libmkl_lapack95_lp64.a -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm
 #Intel parallel openmp (only w/icpc compiler)
 #LINKERFLAGS =  -L$(MKLROOT)/lib/em64t -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lpthread -lm
-LINKERFLAGS =  -L$(MKLROOT)/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lpthread -lm
+LINKERFLAGS =  -static -L$(MKLROOT)/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lpthread -lm
 # MAC OS linkers
 #LINKERFLAGS = -lm -framework Accelerate
 
 
-OFLAGS =  # optimization
+OFLAGS =  -axAVX -xHOST -fast # optimization
 
 
 
diff --git a/ProjectName.cmake b/ProjectName.cmake
index 71ed899..352ea79 100644
--- a/ProjectName.cmake
+++ b/ProjectName.cmake
@@ -1 +1,3 @@
 SET(PROJECT_NAME GSM)
+set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
+set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++")
\ No newline at end of file