********> update.3
  Author: Istvan Kolossvary
  Date:   15 June 2015

  Programs: nab, sff

  Description: Fix problem with lmod docking when fixed atoms are present

  ---------------------------------------------------------------------------

diff --git AmberTools/src/sff/lmodC.c AmberTools/src/sff/lmodC.c
index 8a19dd8..45c8244 100644
--- AmberTools/src/sff/lmodC.c
+++ AmberTools/src/sff/lmodC.c
@@ -864,7 +864,7 @@ trans_ligand(double *xyz, int start, int end, double dx, double dy,
              double dz)
 {
    int i, x, y, z;
-   for (i = start - 1; i < end; i++) {
+   for (i = start; i <= end; i++) {
       x = 3 * i;
       y = x + 1;
       z = y + 1;
@@ -900,7 +900,7 @@ rot_ligand(double *xyz, int start, int end, double cent_x, double cent_y,
 {
    int i, x, y, z;
    double temp_x, temp_y, temp_z;
-   for (i = start - 1; i < end; i++) {
+   for (i = start; i <= end; i++) {
       x = 3 * i;
       y = x + 1;
       z = y + 1;
@@ -930,7 +930,7 @@ calc_centroid(double *xyz, int start, int end, double *cent_x,
 {
    int i, x, y, z, n;
    *cent_x = *cent_y = *cent_z = ZERO;
-   for (i = start - 1; i < end; i++) {
+   for (i = start; i <= end; i++) {
       x = 3 * i;
       y = x + 1;
       z = y + 1;
@@ -1591,6 +1591,7 @@ lmodC(int *nlmodit, int *nmod, int *kmod, int *rotran, int *natm_ext,
        i, j, k, kk, l, n, cnt;
    static int barrier_crossing_test_on, do_all, do_ligs;
    static int *index = NULL;
+   static int ikk, lig_start_kk, lig_end_kk, lig_rot_cent_kk;
    static double ref_energy, energy, energy_old, min_energy,
        glob_min_energy, rad, sum, max_atmov, scale, lmod_step, rms,
        rms_old, grad_rms;
@@ -2554,7 +2555,19 @@ lmodC(int *nlmodit, int *nmod, int *kmod, int *rotran, int *natm_ext,
                xtrans *= trscale / trnorm;
                ytrans *= trscale / trnorm;
                ztrans *= trscale / trnorm;
-               trans_ligand(xyz_local, lig_start[kk], lig_end[kk], xtrans,
+               for (ikk = 0; ikk < natm_local; ikk++ ) {
+                 if ( atm_indx[ikk] == (lig_start[kk] -1) ) {  /* lig_start[] contains external PDB atom numbers */
+                   lig_start_kk = ikk;
+                   break;
+                 }
+               }
+               for (ikk = 0; ikk < natm_local; ikk++ ) {
+                 if ( atm_indx[ikk] == (lig_end[kk] -1) ) {  /* lig_end[] contains external PDB atom numbers */
+                   lig_end_kk = ikk;
+                   break;
+                 }
+               }
+               trans_ligand(xyz_local, lig_start_kk, lig_end_kk, xtrans,
                             ytrans, ztrans);
                do {
                   xrot = 2 * rand2() - 1;
@@ -2568,13 +2581,19 @@ lmodC(int *nlmodit, int *nmod, int *kmod, int *rotran, int *natm_ext,
                rotang = angmin[kk] + (angmax[kk] - angmin[kk]) * rand2();
                calc_rot_matrix(DEG2RAD * rotang, xrot, yrot, zrot, rotmat);
                if (lig_rot_cent[kk]) {
-                  xcent = xyz_local[(lig_rot_cent[kk] - 1) * 3    ];
-                  ycent = xyz_local[(lig_rot_cent[kk] - 1) * 3 + 1];
-                  zcent = xyz_local[(lig_rot_cent[kk] - 1) * 3 + 2];
+                 for (ikk = 0; ikk < natm_local; ikk++ ) {
+                   if ( atm_indx[ikk] == (lig_rot_cent[kk] -1)   ) {  /* lig_rot_cent[] contains external PDB atom numbers */
+                     lig_rot_cent_kk = ikk;
+                     break;
+                   }
+                 }
+                 xcent = xyz_local[ lig_rot_cent_kk * 3    ];
+                 ycent = xyz_local[ lig_rot_cent_kk * 3 + 1];
+                 zcent = xyz_local[ lig_rot_cent_kk * 3 + 2];
                } else
-                  calc_centroid(xyz_local, lig_start[kk], lig_end[kk],
+                  calc_centroid(xyz_local, lig_start_kk, lig_end_kk,
                                 &xcent, &ycent, &zcent);
-               rot_ligand(xyz_local, lig_start[kk], lig_end[kk], xcent,
+               rot_ligand(xyz_local, lig_start_kk, lig_end_kk, xcent,
                           ycent, zcent, rotmat);
             }
             /* close pair separation operates on xyz_ext[]: */