diff --git a/src/main/java/proteomics/Index/BuildIndex.java b/src/main/java/proteomics/Index/BuildIndex.java
index fc23239..58d10be 100644
--- a/src/main/java/proteomics/Index/BuildIndex.java
+++ b/src/main/java/proteomics/Index/BuildIndex.java
@@ -589,7 +589,7 @@ private void getVarModParams(String v, Set<VarModParam> varModParamSet, Set<Bina
                     binaryModParamSet.add(new BinaryModParam(modMass, aas));
                 } else {
                     for (int i = 0; i < aas.length(); ++i) {
-                        if (!fix_mod_map.containsKey(aas.charAt(i))) {
+                        if (Math.abs(fix_mod_map.get(aas.charAt(i))) <= varModMassResolution) {
                             varModParamSet.add(new VarModParam(modMass, aas.charAt(i)));
                         }
                     }