Tue Oct 11 03:23:53 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 03:23:54 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3852 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5213826 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -37.55100 29.69800 ymin,ymax (A): -42.04200 20.24900 zmin,zma (A): -44.76800 23.51200 x,y,z range (A): 67.24900 62.29100 68.28000 scale (grids/A): 0.5213826 object centre (A): -3.926501 -10.89650 -10.62800 number of atom coordinates read : 3852 total number of charged atoms : 3710 net assigned charge : -5.499969 assigned positive charge : 571.8396 centred at (gu) : 89.93615 89.54616 87.74742 assigned negative charge : -577.3418 centred at (gu) : 89.88366 89.56075 87.69339 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 7039 nv = 96 ne = 84 npr = 74419 no. pairs analyzed = 74419 no. exposed pairs = 5272 no. arc points = 37638 no. surface atoms = 1763 nbur = 2089 mkacc time = 0.2100000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 265 mr = 3442 m= 0 mr = 5 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 3857 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3734 ## 554 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 9221 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.3660532E-10 2.9248055E-11 midg,1,midg; midg,igrid,midg -8.0618991E-11 -1.4947213E-10 1,midg,midg; igrid,midg,midg -2.9757838E-10 4.9723576E-11 gauss-seidel spectral radius is 0.9811363 estimated iterations to convergence 60 setup time was (sec) 0.7700000 now iterating at: 03:23:55 rms-change max change #iterations 6.7628317E-02 9.959410 at 10iterations 4.1827336E-03 0.6904387 at 20iterations 4.5705662E-04 7.3266506E-02 at 30iterations 1.1624371E-04 2.1304131E-02 at 40iterations 3.3638931E-05 6.3214302E-03 at 50iterations finished qdiffx linear iterations at : 03:23:58 total time elapsed so far: 4.350000 # loops : 50 mean,max change (kT/e) : 3.3638931E-05 6.3214302E-03 energy calculations done at 4.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.530000 DelPhi exited at 03:23:59 4.532u 0.301s 0:05.21 92.7% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 03:23:59 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3852 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.564148 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -37.55100 29.69800 ymin,ymax (A): -42.04200 20.24900 zmin,zma (A): -44.76800 23.51200 x,y,z range (A): 67.24900 62.29100 68.28000 scale (grids/A): 1.564148 object centre (A): -3.926501 -10.89650 -10.62800 number of atom coordinates read : 3852 total number of charged atoms : 3710 net assigned charge : -5.499969 assigned positive charge : 571.8396 centred at (gu) : 89.80756 88.63753 83.24162 assigned negative charge : -577.3418 centred at (gu) : 89.65052 88.68180 83.07975 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 77813 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37638 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 23495 mr = 50854 m= 2264 mr = 15753 m= 61 mr = 950 m= 0 mr = 3 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 1175 time to turn everything in is 0.5900000 number of dielectric boundary points 36073 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 465 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 28070 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5213826 object centre at (A) : -3.926501 -10.89650 -10.62800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3401519E-02 9.2504984E-03 midg,1,midg; midg,igrid,midg -4.4585117E-03 -3.5324711E-03 1,midg,midg; igrid,midg,midg -1.9696022E-04 2.1292249E-02 gauss-seidel spectral radius is 0.9981337 estimated iterations to convergence 184 setup time was (sec) 0.9200000 now iterating at: 03:24:00 rms-change max change #iterations 3.504561 163.4407 at 10iterations 1.431357 55.96217 at 20iterations 0.5886780 20.24665 at 30iterations 0.2426692 8.030727 at 40iterations 9.9698290E-02 4.067673 at 50iterations 4.1138463E-02 1.455542 at 60iterations 1.6954811E-02 0.5313473 at 70iterations 7.0397686E-03 0.2394304 at 80iterations 2.9540821E-03 0.1137886 at 90iterations 1.2721255E-03 4.2034149E-02 at 100iterations 5.8009353E-04 2.1958351E-02 at 110iterations 2.8713013E-04 1.0720730E-02 at 120iterations finished qdiffx linear iterations at : 03:24:09 total time elapsed so far: 9.560000 # loops : 120 mean,max change (kT/e) : 2.8713013E-04 1.0720730E-02 energy calculations done at 9.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.750000 DelPhi exited at 03:24:09 9.749u 0.263s 0:10.34 96.7% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 03:24:09 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3852 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.346221 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -37.55100 29.69800 ymin,ymax (A): -42.04200 20.24900 zmin,zma (A): -44.76800 23.51200 x,y,z range (A): 67.24900 62.29100 68.28000 scale (grids/A): 2.346221 object centre (A): -3.926501 -10.89650 -10.62800 number of atom coordinates read : 3852 total number of charged atoms : 3710 net assigned charge : -5.499969 assigned positive charge : 571.8396 centred at (gu) : 89.71120 87.95605 79.86208 assigned negative charge : -577.3418 centred at (gu) : 89.47572 88.02264 79.61940 start vw surface at 0.1800000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 180543 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37638 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 82009 mr = 125054 m= 22382 mr = 63727 m= 3236 mr = 16297 m= 209 mr = 1858 m= 3 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 4111 time to turn everything in is 1.430000 number of dielectric boundary points 81383 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 50 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 29606 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.564148 object centre at (A) : -3.926501 -10.89650 -10.62800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2766582 0.1684001 midg,1,midg; midg,igrid,midg -3.2720163E-02 -1.0424569E-02 1,midg,midg; igrid,midg,midg 7.7246323E-02 0.7629269 gauss-seidel spectral radius is 0.9991590 estimated iterations to convergence 272 setup time was (sec) 1.780000 now iterating at: 03:24:11 rms-change max change #iterations 9.429614 300.3994 at 10iterations 5.371776 131.8770 at 20iterations 3.045784 80.72784 at 30iterations 1.716286 36.42271 at 40iterations 0.9634949 22.69222 at 50iterations 0.5376382 10.88521 at 60iterations 0.3018102 6.274922 at 70iterations 0.1682317 3.977470 at 80iterations 9.3514271E-02 1.887627 at 90iterations 5.2045926E-02 1.050093 at 100iterations 2.8923703E-02 0.5636129 at 110iterations 1.6073108E-02 0.2963166 at 120iterations 8.9342259E-03 0.1824379 at 130iterations 4.9503380E-03 0.1053958 at 140iterations 2.7605479E-03 5.7191849E-02 at 150iterations 1.5384209E-03 3.1513214E-02 at 160iterations 8.6240622E-04 1.7985344E-02 at 170iterations 4.8918882E-04 9.8257065E-03 at 180iterations finished qdiffx linear iterations at : 03:24:25 total time elapsed so far: 15.53000 # loops : 180 mean,max change (kT/e) : 4.8918882E-04 9.8257065E-03 energy calculations done at 15.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.71000 DelPhi exited at 03:24:26 15.714u 0.280s 0:16.30 98.0% 0+0k 0+0io 0pf+0w