diff -rupN autodock-src-ref/autodock/AD4.1_bound.dat autodock-src-mod/autodock/AD4.1_bound.dat
--- autodock-src-ref/autodock/AD4.1_bound.dat	2015-05-12 12:31:14.339137615 +0300
+++ autodock-src-mod/autodock/AD4.1_bound.dat	2015-06-01 17:29:30.113177641 +0300
@@ -118,3 +118,4 @@ atom_par G      4.00  0.150  33.5103  -0
 atom_par GA     4.00  0.150  33.5103  -0.00052  0.0  0.0  0  -1  -1  0	# Ring closure Glue Aromatic Carbon   # SF
 atom_par J      4.00  0.150  33.5103  -0.00143  0.0  0.0  0  -1  -1  0	# Ring closure Glue Aliphatic Carbon  # SF
 atom_par Q      4.00  0.150  33.5103  -0.00143  0.0  0.0  0  -1  -1  0	# Ring closure Glue Aliphatic Carbon  # SF
+atom_par Xx     0.10  0.000     0.00   0.00000  0.0  0.0  0  -1  -1  4  # Dummy atoms
diff -rupN autodock-src-ref/autodock/AD4.1_compact.dat autodock-src-mod/autodock/AD4.1_compact.dat
--- autodock-src-ref/autodock/AD4.1_compact.dat	2015-05-12 12:31:14.339137615 +0300
+++ autodock-src-mod/autodock/AD4.1_compact.dat	2015-06-01 17:29:30.429178066 +0300
@@ -118,3 +118,4 @@ atom_par G      4.00  0.150  33.5103  -0
 atom_par GA     4.00  0.150  33.5103  -0.00052  0.0  0.0  0  -1  -1  0	# Ring closure Glue Aromatic Carbon   # SF
 atom_par J      4.00  0.150  33.5103  -0.00143  0.0  0.0  0  -1  -1  0	# Ring closure Glue Aliphatic Carbon  # SF
 atom_par Q      4.00  0.150  33.5103  -0.00143  0.0  0.0  0  -1  -1  0	# Ring closure Glue Aliphatic Carbon  # SF
+atom_par Xx     0.10  0.000     0.00   0.00000  0.0  0.0  0  -1  -1  4  # Dummy atoms
diff -rupN autodock-src-ref/autodock/AD4.1_extended.dat autodock-src-mod/autodock/AD4.1_extended.dat
--- autodock-src-ref/autodock/AD4.1_extended.dat	2015-05-12 12:31:14.339137615 +0300
+++ autodock-src-mod/autodock/AD4.1_extended.dat	2015-06-01 17:29:30.463178112 +0300
@@ -118,3 +118,4 @@ atom_par G      4.00  0.150  33.5103  -0
 atom_par GA     4.00  0.150  33.5103  -0.00052  0.0  0.0  0  -1  -1  0	# Ring closure Glue Aromatic Carbon   # SF
 atom_par J      4.00  0.150  33.5103  -0.00143  0.0  0.0  0  -1  -1  0	# Ring closure Glue Aliphatic Carbon  # SF
 atom_par Q      4.00  0.150  33.5103  -0.00143  0.0  0.0  0  -1  -1  0	# Ring closure Glue Aliphatic Carbon  # SF
+atom_par Xx     0.10  0.000     0.00   0.00000  0.0  0.0  0  -1  -1  4  # Dummy atoms
diff -rupN autodock-src-ref/autodock/AD4_parameters.dat autodock-src-mod/autodock/AD4_parameters.dat
--- autodock-src-ref/autodock/AD4_parameters.dat	2015-05-12 12:31:14.339137615 +0300
+++ autodock-src-mod/autodock/AD4_parameters.dat	2015-06-01 17:29:30.493178152 +0300
@@ -116,3 +116,4 @@ atom_par G      4.00  0.150  33.5103  -0
 atom_par GA     4.00  0.150  33.5103  -0.00052  0.0  0.0  0  -1  -1  0	# Ring closure Glue Aromatic Carbon   # SF
 atom_par J      4.00  0.150  33.5103  -0.00143  0.0  0.0  0  -1  -1  0	# Ring closure Glue Aliphatic Carbon  # SF
 atom_par Q      4.00  0.150  33.5103  -0.00143  0.0  0.0  0  -1  -1  0	# Ring closure Glue Aliphatic Carbon  # SF
+atom_par Xx     0.10  0.000     0.00   0.00000  0.0  0.0  0  -1  -1  4  # Dummy atoms
diff -rupN autodock-src-ref/autodock/AD4_PARM99.dat autodock-src-mod/autodock/AD4_PARM99.dat
--- autodock-src-ref/autodock/AD4_PARM99.dat	2015-05-12 12:31:14.339137615 +0300
+++ autodock-src-mod/autodock/AD4_PARM99.dat	2015-06-01 17:29:30.569178254 +0300
@@ -92,3 +92,4 @@ atom_par G      4.00  0.086    29.10  -0
 atom_par GA     4.00  0.086    29.10  -0.00052  0.0  0.0  0  -1  -1  0	# Ring closure Glue Aromatic Carbon   # SF
 atom_par J      4.00  0.086    29.10  -0.00143  0.0  0.0  0  -1  -1  0	# Ring closure Glue Aliphatic Carbon  # SF
 atom_par Q      4.00  0.086    29.10  -0.00143  0.0  0.0  0  -1  -1  0	# Ring closure Glue Aliphatic Carbon  # SF
+atom_par Xx     0.10  0.000     0.00   0.00000  0.0  0.0  0  -1  -1  4  # Dummy atoms
diff -rupN autodock-src-ref/autodock/main.cc autodock-src-mod/autodock/main.cc
--- autodock-src-ref/autodock/main.cc	2015-05-12 12:31:14.342137717 +0300
+++ autodock-src-mod/autodock/main.cc	2015-06-01 17:29:30.082177600 +0300
@@ -1589,6 +1589,40 @@ while( fgets(line, LINE_LEN, parFile) !=
             abs_charge[i] = fabs(charge[i]);
             qsp_abs_charge[i] = qsolpar * abs_charge[i];
         }
+        // modify solvation charges to take MCCs into account
+#define MCC_DISTANCE(a, b) sqrt(((a)[0]-(b)[0])*((a)[0]-(b)[0])+((a)[1]-(b)[1])*((a)[1]-(b)[1])+((a)[2]-(b)[2])*((a)[2]-(b)[2]))
+        { // put everything in a block to avoid namespace pollution
+            int mcc_list[MAX_ATOMS][6]; // first index is a root of mcc
+            float mcc_max_radius = 0.15f;
+            for (i=0;i<true_ligand_atoms;++i) {
+                for (int j = 0; j < 6; j++) mcc_list[i][j]=-1;
+            }
+            for (i=0; i<true_ligand_atoms; i++) {
+                // check if atom is a part of mcc
+                int found = 0;
+                for (int k=0;k<true_ligand_atoms;++k) for (int l = 0; l < 6; l++) if (mcc_list[k][l]==i) found = 1;
+                if (found) continue;
+                int cur_position = 0;
+                for (int j = i+1; j < true_ligand_atoms; ++j) {
+                    if ( MCC_DISTANCE(crdorig[i],crdorig[j]) < mcc_max_radius ) {
+                      mcc_list[i][cur_position] = j;
+                      ++cur_position;
+                    }
+                }
+            }
+            // reduce MCC to a single atom
+            for (i=0; i<true_ligand_atoms; i++) {
+                for(int j = 0; j < 6; ++j) {
+                    if (mcc_list[i][j] != -1) {
+                        qsp_abs_charge[i] -= qsp_abs_charge[mcc_list[i][j]];
+                        qsp_abs_charge[mcc_list[i][j]] = 0.0;
+                        abs_charge[i] -= abs_charge[mcc_list[i][j]];
+                        abs_charge[mcc_list[i][j]] = 0.0;
+                    }
+                }
+            }
+        }
+#undef MCC_DISTANCE
         pr(logFile, "Number of atoms in ligand:  %d\n\n", true_ligand_atoms);
         pr(logFile, "Number of non-hydrogen atoms in ligand:  %d\n\n", n_heavy_atoms_in_ligand);
 
