diff --git a/src/EXTRA-COMMAND/ndx_group.cpp b/src/EXTRA-COMMAND/ndx_group.cpp
index c5b0d3cf8a..d006473bb8 100644
--- a/src/EXTRA-COMMAND/ndx_group.cpp
+++ b/src/EXTRA-COMMAND/ndx_group.cpp
@@ -33,7 +33,8 @@ static std::string find_section(FILE *fp, const std::string &name)
 {
   char linebuf[BUFLEN];
 
-  fgets(linebuf, BUFLEN, fp);
+  if (!fgets(linebuf, BUFLEN, fp))
+    throw TokenizerException("Read error", utils::getsyserror());
   while (!feof(fp)) {
     if (utils::strmatch(linebuf, "^\\s*\\[.*\\]\\s*$")) {
       auto words = Tokenizer(linebuf).as_vector();
diff --git a/src/angle_write.cpp b/src/angle_write.cpp
index 48420ae7be..1be5f1acac 100644
--- a/src/angle_write.cpp
+++ b/src/angle_write.cpp
@@ -148,8 +148,10 @@ void AngleWrite::command(int narg, char **arg)
     FILE *coeffs;
     char line[MAXLINE] = {'\0'};
     coeffs = fopen(coeffs_file.c_str(), "r");
+    if (!coeffs)
+      error->one(FLERR, "Unable to open temporary file {}: {}", coeffs_file, utils::getsyserror());
     for (int i = 0; i < atom->nangletypes; ++i) {
-      fgets(line, MAXLINE, coeffs);
+      utils::sfgets(FLERR, line, MAXLINE, coeffs, coeffs_file.c_str(), error);
       writer->input->one(fmt::format("angle_coeff {}", line));
     }
     fclose(coeffs);
diff --git a/src/dihedral_write.cpp b/src/dihedral_write.cpp
index dd1ca1de6a..1d0f908e2c 100644
--- a/src/dihedral_write.cpp
+++ b/src/dihedral_write.cpp
@@ -149,8 +149,10 @@ void DihedralWrite::command(int narg, char **arg)
     FILE *coeffs;
     char line[MAXLINE] = {'\0'};
     coeffs = fopen(coeffs_file.c_str(), "r");
+    if (!coeffs)
+      error->one(FLERR, "Unable to open temporary file {}: {}", utils::getsyserror());
     for (int i = 0; i < atom->ndihedraltypes; ++i) {
-      fgets(line, MAXLINE, coeffs);
+      utils::sfgets(FLERR, line, MAXLINE, coeffs, coeffs_file.c_str(), error);
       writer->input->one(fmt::format("dihedral_coeff {}", line));
     }
     fclose(coeffs);
diff --git a/tools/msi2lmp/src/ReadMdfFile.c b/tools/msi2lmp/src/ReadMdfFile.c
index 96a6a01ab2..253121d001 100644
--- a/tools/msi2lmp/src/ReadMdfFile.c
+++ b/tools/msi2lmp/src/ReadMdfFile.c
@@ -144,7 +144,7 @@ void ReadMdfFile(void)
 
         molecule[n].residue[j].end = i;
         molecule[n].residue[++j].start = i;
-        strncpy(molecule[n].residue[j].name,atoms[i].residue_string,MAX_NAME);
+        memcpy(molecule[n].residue[j].name,atoms[i].residue_string,MAX_NAME);
       }
     }
     molecule[n].residue[j].end = molecule[n].end;
@@ -167,10 +167,9 @@ void ReadMdfFile(void)
 
   for (n=0; n < no_molecules; n++) {
     for (j=0; j < molecule[n].no_residues; j++) {
-      for (i=molecule[n].residue[j].start; i < molecule[n].residue[j].end;
-           i++) {
+      for (i=molecule[n].residue[j].start; i < molecule[n].residue[j].end; i++) {
         for (l=0; l < atoms[i].no_connect; l++) {
-          strncpy(temp_string,atoms[i].connections[l],MAX_STRING);
+          memcpy(temp_string,atoms[i].connections[l],MAX_STRING);
           temp_residue = strtok(temp_string,":");
           temp_atom_name = strtok(NULL,"%");