diff options
Diffstat (limited to 'sci-chemistry/ambertools/files/ambertools-15-update.3.patch')
| -rw-r--r-- | sci-chemistry/ambertools/files/ambertools-15-update.3.patch | 95 |
1 files changed, 95 insertions, 0 deletions
diff --git a/sci-chemistry/ambertools/files/ambertools-15-update.3.patch b/sci-chemistry/ambertools/files/ambertools-15-update.3.patch new file mode 100644 index 000000000..a892ecefd --- /dev/null +++ b/sci-chemistry/ambertools/files/ambertools-15-update.3.patch @@ -0,0 +1,95 @@ +********> 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[]: */ |