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********> 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[]: */
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