diff --git a/output.dat b/AAoutput.dat
similarity index 100%
rename from output.dat
rename to AAoutput.dat
diff --git a/CommonRoutines.H b/CommonRoutines.H
index c56b53b..6b12f5d 100644
--- a/CommonRoutines.H
+++ b/CommonRoutines.H
@@ -53,9 +53,9 @@ bool getDoubleFromString(double &retVal, string s,
 
 bool getDouble(double &retVal, double defaultValue);
 
-bool getInt(int &retVal, int defaultValue);
+bool getInt(long int &retVal, int defaultValue);
 
-bool getIntFromString(int &retVal, string s, int lowBounds, int hiBounds);
+bool getIntFromString(long int &retVal, string s, int lowBounds, long int hiBounds);
 
 int getIntInput(string prompt, int defaultVal, int lowBounds, int hiBounds);
 
@@ -78,7 +78,7 @@ bool fileExists(string fn);
 void getValidDoubleTokens (double &retVal, ifstream &ifs, double low,
                            double hi, string validLabel, int errorCode);
 
-void getValidIntTokens (int &retVal, ifstream &ifs, int low,
+void getValidIntTokens (long int &retVal, ifstream &ifs, int low,
                         int hi, string validLabel, int errorCode);
 
 void getValidCharTokens (string &retVal, ifstream &ifs,
@@ -103,5 +103,3 @@ int findAAindex(char ch);
 //===========================================================================
 //=======================  END OF CommonRoutines.H   ========================
 //===========================================================================
-
-
diff --git a/CommonRoutines.cpp b/CommonRoutines.cpp
index 306280f..410172e 100644
--- a/CommonRoutines.cpp
+++ b/CommonRoutines.cpp
@@ -35,9 +35,11 @@
 #include <iostream>
 #include <fstream>
 #include <vector>
+#include <cstring>
 #include "CommonRoutines.H"
 using namespace std;
 
+const long int HI_BOUND = 1000000000000000001;
 
 //---------------------------------------------------------------------------
 bool isNum(char ch) {
@@ -85,7 +87,7 @@ bool getDoubleFromString(double &retVal, string s,
    lhTok = strtok((char *)s.c_str(), ".");
    rhTok = strtok(NULL, "\n");
 
-   int lhs, rhs;
+   long int lhs, rhs;
    if(rhTok == NULL) {
       if(getIntFromString(lhs, lhTok, -1, 101)) {
          retVal = (double) lhs;
@@ -96,8 +98,10 @@ bool getDoubleFromString(double &retVal, string s,
       }
    }
 
+   // cout << "rhTok: " << rhTok << endl;
+   // cout << "getIntFromString: " << getIntFromString(rhs, rhTok, -1, HI_BOUND) << endl;
    if(getIntFromString(lhs, lhTok, -1, 101) &&
-      getIntFromString(rhs, rhTok, -1, 10001)) {
+      getIntFromString(rhs, rhTok, -1, HI_BOUND)) {
 
       // rhs should be divided accordingly
       int divisor = 1;
@@ -118,7 +122,7 @@ bool getDoubleFromString(double &retVal, string s,
 //---------------------------------------------------------------------------
 
 //---------------------------------------------------------------------------
-bool getIntFromString(int &retVal, string s, int lowBounds, int hiBounds) {
+bool getIntFromString(long int &retVal, string s, int lowBounds, long int hiBounds) {
 
    //**********************************************************************
    // PRE  : defaultValue has been set
@@ -139,10 +143,16 @@ bool getIntFromString(int &retVal, string s, int lowBounds, int hiBounds) {
       if(!isNum(currCh))
          return(false);
       else {
-         int currMult = (int)pow(10,len-i-1);
-         retVal += currMult * ((int)currCh - 48);
+         long int currMult = (long int)pow(10,len-i-1);
+         retVal += currMult * ((long int)currCh - 48);
       }
    }
+
+   // Debugging purpose
+   // cout << "retVal: " << retVal << endl;
+   // cout << "lowBounds: " << lowBounds << endl;
+   // cout << "hiBounds: " << hiBounds << endl;
+   // cout << "(retVal > lowBounds)  && (retVal < hiBounds): " << ((retVal > lowBounds)  && (retVal < hiBounds)) << endl;
    if((retVal > lowBounds)  && (retVal < hiBounds))
       return(true);
    else
@@ -196,7 +206,7 @@ bool getDouble(double &retVal, double defaultValue) {
 //---------------------------------------------------------------------------
 
 //---------------------------------------------------------------------------
-bool getInt(int &retVal, int defaultValue) {
+bool getInt(long int &retVal, int defaultValue) {
 
    //**********************************************************************
    // PRE  : defaultValue has been set
@@ -377,7 +387,7 @@ void getValidDoubleTokens (double &retVal, ifstream &ifs, double low,
 //---------------------------------------------------------------------------
 
 //---------------------------------------------------------------------------
-void getValidIntTokens (int &retVal, ifstream &ifs, int low,
+void getValidIntTokens (long int &retVal, ifstream &ifs, int low,
                         int hi, string validLabel, int errorCode) {
 
    //**********************************************************************
@@ -449,7 +459,7 @@ int getIntInput(string prompt, int defaultVal, int lowBounds, int hiBounds) {
    //**********************************************************************
 
    bool finished = false;
-   int retVal;
+   long int retVal;
 
    while(!finished) {
       cout << prompt;
@@ -688,5 +698,3 @@ int findAAindex(char ch) {
 //===========================================================================
 //=====================  END OF CommonRoutines.cpp ==========================
 //===========================================================================
-
-
diff --git a/Makefile b/Makefile
index c49a584..cf08cc7 100644
--- a/Makefile
+++ b/Makefile
@@ -1,5 +1,5 @@
 COMPILER = g++
-CCFLAGS = -g
+CCFLAGS = -g -fpermissive
 
 rMotifGen: RandomMotifs.cpp SequenceClass.o CommonRoutines.o SubstitutionMatrices.o PSSM.o
 	${COMPILER} ${CCFLAGS} -o rMotifGen RandomMotifs.cpp SequenceClass.o CommonRoutines.o SubstitutionMatrices.o PSSM.o
diff --git a/PSSM.cpp b/PSSM.cpp
index 7ec0e8e..f29f966 100644
--- a/PSSM.cpp
+++ b/PSSM.cpp
@@ -112,6 +112,7 @@ void PSSM::checkForValidPSSM() {
    else {
       if(!checkColOrientation()) {
          if(!checkRowOrientation()) {
+            cerr << "Invalid orientation" << endl;
             errorVal = 29; // INCORRECTLY FORMATTED PSSM FILE
             return;
          }
@@ -205,6 +206,7 @@ bool PSSM::checkColOrientation() {
          double tmpD;
          ss >> tmpS;
          if(!getDoubleFromString(tmpD, tmpS, 0.0, 10000.0)) {
+            cerr << "Invalid string reading in col orientation"  << endl;
             errorVal = 29;
             return(false);
          }
@@ -286,6 +288,7 @@ bool PSSM::checkRowOrientation() {
          // MAKE SURE EACH COLUMN IS A POSITIVE DOUBLE VALUE
 
          if(!getDoubleFromString(tmpD, tmpS, 0.0, 10000.0)) {
+            cerr << "Invalid string reading in row orientation" << endl;
             errorVal = 29;
             return(false);
          }
diff --git a/README b/README
index 18502c2..ba0164f 100644
--- a/README
+++ b/README
@@ -107,6 +107,7 @@ RUNNING rMotifGen
         motif<X>Type=      // Where X=1..numMotifs --  the value can
                            // be 'U' for user defined, 'R' for random
                            // or 'P' for PSSM
+        motif<X>PSSMFILE=  // PSSM filename if motif<X>Type=P
         motif<X>Seq=       // Only Valid if Type = 'U' -- consensus motif
         motif<X>PctSeqsContain= // Percentage of sequences that contain this 
                                 // motif 
diff --git a/RandomMotifs.cpp b/RandomMotifs.cpp
index 9d66902..5e59a90 100644
--- a/RandomMotifs.cpp
+++ b/RandomMotifs.cpp
@@ -505,7 +505,7 @@ void getRandomMotifInfo(ifstream &infile, char *&motif_createTypeArr,
     string motifLabel = setMotifLabel(i);
     string currLabel = motifLabel + "Len";
 
-    int tmpint;
+    long int tmpint;
     if(infile.eof()) { exit(26); }
     getValidIntTokens(tmpint, infile, 0, 101, currLabel, 18);
     motif_lenArr[i] = tmpint;
@@ -580,7 +580,7 @@ void getPAMValue(PAM **&motif_PAMArr, ifstream &infile,
    //**********************************************************************
 
     string currLabel = motifLabel + "PAM";
-    int pamVal;
+    long int pamVal;
     if(infile.eof()) { exit(26); }
     getValidIntTokens(pamVal, infile, -1, 501, currLabel, 17);
     motif_PAMArr[i] = new PAM(pamVal);
@@ -601,9 +601,9 @@ void fileMode(string FN, char seqType){
 
    double *ResiduePcts;
    char   *ResidueLabels;
-   int seqLen;
-   int numMotifs;
-   int numSeqs;
+   long int seqLen;
+   long int numMotifs;
+   long int numSeqs;
    bool finished;
    char   *motif_createTypeArr;
    bool   *motif_isPalindromicArr;
@@ -675,7 +675,7 @@ void fileMode(string FN, char seqType){
          }
          motif_PSSMArr[i] = currPSSM;
          currLabel = motifLabel + "PctSeqsContain";
-         int tmpint;
+         long int tmpint;
          if(infile.eof()) { exit(26); }
          getValidIntTokens(tmpint, infile, -1, 101, currLabel, 16);
           motif_pctSeqConsArr[i] = tmpint;
@@ -872,7 +872,3 @@ int main(int argc, char *argv[]) {
 //============================================================================
 //--------------------------- END OF RandomMotifs.cpp ------------------------
 //============================================================================
-
-
-
-
diff --git a/SequenceClass.cpp b/SequenceClass.cpp
index 45c121f..92035c1 100644
--- a/SequenceClass.cpp
+++ b/SequenceClass.cpp
@@ -144,7 +144,7 @@ string SequenceClass::randomPSSMSeq(PSSM *P) {
          }
       }
       if(!nextFound) {
-         s+= P->residueArr[P->totRows - 1];
+         s+= P->residueArr[P->totCols - 1];
       }
    }
    return(s);