Tue Oct 11 08:32:50 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 08:32:50 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 = 2120 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7334157 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): 41.26300 88.46301 ymin,ymax (A): -28.90400 13.25400 zmin,zma (A): -3.033000 45.50700 x,y,z range (A): 47.20001 42.15800 48.54000 scale (grids/A): 0.7334157 object centre (A): 64.86300 -7.825000 21.23700 number of atom coordinates read : 2120 total number of charged atoms : 1992 net assigned charge : 6.500009 assigned positive charge : 322.2599 centred at (gu) : 89.17711 89.72885 90.59895 assigned negative charge : -315.7602 centred at (gu) : 89.30096 89.64372 90.53098 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7868 nv = 96 ne = 84 npr = 42527 no. pairs analyzed = 42527 no. exposed pairs = 2457 no. arc points = 16867 no. surface atoms = 841 nbur = 1279 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 545 mr = 4735 m= 4 mr = 114 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.1800000 number of dielectric boundary points 3568 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1417 ## 119 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8288 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4696178E-08 1.7577305E-07 midg,1,midg; midg,igrid,midg 2.3899698E-08 1.6349803E-07 1,midg,midg; igrid,midg,midg 2.3962852E-07 -9.0354506E-09 gauss-seidel spectral radius is 0.9903058 estimated iterations to convergence 83 setup time was (sec) 0.3700000 now iterating at: 08:32:51 rms-change max change #iterations 0.2361991 33.23352 at 10iterations 3.1907257E-02 3.709381 at 20iterations 4.2962013E-03 0.5519638 at 30iterations 6.4674561E-04 8.0205917E-02 at 40iterations 1.2958529E-04 1.8020630E-02 at 50iterations finished qdiffx linear iterations at : 08:32:54 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.2958529E-04 1.8020630E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 08:32:54 3.410u 0.177s 0:04.09 87.5% 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 08:32:55 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 = 2120 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.200247 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): 41.26300 88.46301 ymin,ymax (A): -28.90400 13.25400 zmin,zma (A): -3.033000 45.50700 x,y,z range (A): 47.20001 42.15800 48.54000 scale (grids/A): 2.200247 object centre (A): 64.86300 -7.825000 21.23700 number of atom coordinates read : 2120 total number of charged atoms : 1992 net assigned charge : 6.500009 assigned positive charge : 322.2599 centred at (gu) : 87.53144 89.18642 91.79678 assigned negative charge : -315.7602 centred at (gu) : 87.90285 88.93118 91.59312 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 83440 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16867 grid for indexing accessible points = 1.400000 m= 34786 mr = 60940 m= 6976 mr = 27188 m= 693 mr = 4828 m= 34 mr = 398 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 378 time to turn everything in is 0.4100000 number of dielectric boundary points 32566 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 47 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 15847 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) : 0.7334157 object centre at (A) : 64.86300 -7.825000 21.23700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9891627E-02 5.5279579E-02 midg,1,midg; midg,igrid,midg 3.4859736E-02 3.0308962E-02 1,midg,midg; igrid,midg,midg 5.0111916E-02 -5.2520648E-02 gauss-seidel spectral radius is 0.9989012 estimated iterations to convergence 239 setup time was (sec) 0.6300000 now iterating at: 08:32:55 rms-change max change #iterations 4.991831 207.2517 at 10iterations 2.520565 79.02422 at 20iterations 1.281869 38.19047 at 30iterations 0.6499613 18.41175 at 40iterations 0.3303984 9.230435 at 50iterations 0.1673512 4.839993 at 60iterations 8.5020110E-02 2.724418 at 70iterations 4.3264408E-02 1.153614 at 80iterations 2.1883629E-02 0.6062204 at 90iterations 1.1182675E-02 0.3189316 at 100iterations 5.6988425E-03 0.1529465 at 110iterations 2.9411046E-03 7.8475952E-02 at 120iterations finished qdiffx linear iterations at : 08:33:03 total time elapsed so far: 7.860000 # loops : 120 mean,max change (kT/e) : 2.9411046E-03 7.8475952E-02 energy calculations done at 7.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 08:33:03 7.998u 0.230s 0:08.72 94.2% 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 08:33:03 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 = 2120 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.300371 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): 41.26300 88.46301 ymin,ymax (A): -28.90400 13.25400 zmin,zma (A): -3.033000 45.50700 x,y,z range (A): 47.20001 42.15800 48.54000 scale (grids/A): 3.300371 object centre (A): 64.86300 -7.825000 21.23700 number of atom coordinates read : 2120 total number of charged atoms : 1992 net assigned charge : 6.500009 assigned positive charge : 322.2599 centred at (gu) : 86.29710 88.77948 92.69512 assigned negative charge : -315.7602 centred at (gu) : 86.85432 88.39692 92.38970 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 192242 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16867 grid for indexing accessible points = 1.400000 m= 107731 mr = 145832 m= 45091 mr = 91495 m= 13124 mr = 37892 m= 2681 mr = 10394 m= 394 mr = 1974 m= 25 mr = 284 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 1260 time to turn everything in is 1.300000 number of dielectric boundary points 73417 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 15936 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) : 2.200247 object centre at (A) : 64.86300 -7.825000 21.23700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2028596 0.4449300 midg,1,midg; midg,igrid,midg 0.2990156 0.1560025 1,midg,midg; igrid,midg,midg 0.4996247 -0.6511537 gauss-seidel spectral radius is 0.9993127 estimated iterations to convergence 301 setup time was (sec) 1.520000 now iterating at: 08:33:05 rms-change max change #iterations 10.78839 367.2161 at 10iterations 6.407895 121.3844 at 20iterations 3.793096 73.95628 at 30iterations 2.247141 45.13938 at 40iterations 1.328292 28.82152 at 50iterations 0.7837423 16.33539 at 60iterations 0.4625920 8.221489 at 70iterations 0.2727019 5.010717 at 80iterations 0.1608094 3.009388 at 90iterations 9.4665669E-02 1.697765 at 100iterations 5.5853181E-02 0.9333760 at 110iterations 3.3013124E-02 0.5160589 at 120iterations 1.9567592E-02 0.3485107 at 130iterations 1.1703284E-02 0.2035408 at 140iterations 7.0971111E-03 0.1320486 at 150iterations 4.4251787E-03 8.4941864E-02 at 160iterations 2.8803148E-03 5.0580978E-02 at 170iterations 1.9938860E-03 3.6441803E-02 at 180iterations finished qdiffx linear iterations at : 08:33:17 total time elapsed so far: 12.95000 # loops : 180 mean,max change (kT/e) : 1.9938860E-03 3.6441803E-02 energy calculations done at 12.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.08000 DelPhi exited at 08:33:17 13.083u 0.231s 0:14.05 94.7% 0+0k 0+0io 0pf+0w