Tue Oct 11 03:54:18 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 03:54:19 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 = 2697 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6614887 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): -11.39700 36.71000 ymin,ymax (A): -26.76300 21.55700 zmin,zma (A): -8.264000 45.55400 x,y,z range (A): 48.10700 48.32000 53.81800 scale (grids/A): 0.6614887 object centre (A): 12.65650 -2.603001 18.64500 number of atom coordinates read : 2697 total number of charged atoms : 2549 net assigned charge : 2.500014 assigned positive charge : 407.7948 centred at (gu) : 90.20461 90.30522 91.38457 assigned negative charge : -405.2953 centred at (gu) : 89.90950 90.13174 91.38117 start vw surface at 0.1600000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7889 nv = 96 ne = 84 npr = 55674 no. pairs analyzed = 55674 no. exposed pairs = 3176 no. arc points = 22202 no. surface atoms = 1064 nbur = 1633 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 468 mr = 4601 m= 2 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.3600000 number of dielectric boundary points 3704 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2203 ## 228 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9351 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.3646957E-09 9.5167101E-09 midg,1,midg; midg,igrid,midg -2.9420899E-08 4.5810928E-08 1,midg,midg; igrid,midg,midg -5.6290880E-08 7.0751575E-08 gauss-seidel spectral radius is 0.9881594 estimated iterations to convergence 75 setup time was (sec) 0.6300000 now iterating at: 03:54:19 rms-change max change #iterations 0.1720499 21.27954 at 10iterations 1.8782487E-02 2.239140 at 20iterations 2.0622767E-03 0.2751846 at 30iterations 2.5517136E-04 4.1904449E-02 at 40iterations 4.3455981E-05 5.7907104E-03 at 50iterations finished qdiffx linear iterations at : 03:54:23 total time elapsed so far: 3.910000 # loops : 50 mean,max change (kT/e) : 4.3455981E-05 5.7907104E-03 energy calculations done at 3.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 03:54:23 4.085u 0.265s 0:04.73 91.7% 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 03:54:23 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 = 2697 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.984466 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): -11.39700 36.71000 ymin,ymax (A): -26.76300 21.55700 zmin,zma (A): -8.264000 45.55400 x,y,z range (A): 48.10700 48.32000 53.81800 scale (grids/A): 1.984466 object centre (A): 12.65650 -2.603001 18.64500 number of atom coordinates read : 2697 total number of charged atoms : 2549 net assigned charge : 2.500014 assigned positive charge : 407.7948 centred at (gu) : 90.61338 90.91515 94.15318 assigned negative charge : -405.2953 centred at (gu) : 89.72807 90.39500 94.14294 start vw surface at 0.1400000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 85019 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22202 grid for indexing accessible points = 1.400000 m= 32839 mr = 60920 m= 5536 mr = 24964 m= 353 mr = 3625 m= 2 mr = 151 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 984 time to turn everything in is 0.7400000 number of dielectric boundary points 34089 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 137 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 20119 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) : 0.6614887 object centre at (A) : 12.65650 -2.603001 18.64500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5659878E-02 -1.0281838E-02 midg,1,midg; midg,igrid,midg -1.5687520E-02 3.1040162E-02 1,midg,midg; igrid,midg,midg -1.5804507E-02 7.9814695E-02 gauss-seidel spectral radius is 0.9987447 estimated iterations to convergence 224 setup time was (sec) 1.030000 now iterating at: 03:54:25 rms-change max change #iterations 4.720630 224.7252 at 10iterations 2.294029 68.76699 at 20iterations 1.108240 33.36232 at 30iterations 0.5372941 17.07609 at 40iterations 0.2605051 7.715881 at 50iterations 0.1259617 3.588982 at 60iterations 6.1131161E-02 1.796242 at 70iterations 2.9577740E-02 0.8305273 at 80iterations 1.4338181E-02 0.3956089 at 90iterations 6.9602430E-03 0.1917992 at 100iterations 3.3992208E-03 0.1071715 at 110iterations 1.6614757E-03 5.4251671E-02 at 120iterations finished qdiffx linear iterations at : 03:54:33 total time elapsed so far: 9.390000 # loops : 120 mean,max change (kT/e) : 1.6614757E-03 5.4251671E-02 energy calculations done at 9.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.570000 DelPhi exited at 03:54:34 9.569u 0.318s 0:10.41 94.8% 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 03:54:34 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 = 2697 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.976699 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): -11.39700 36.71000 ymin,ymax (A): -26.76300 21.55700 zmin,zma (A): -8.264000 45.55400 x,y,z range (A): 48.10700 48.32000 53.81800 scale (grids/A): 2.976699 object centre (A): 12.65650 -2.603001 18.64500 number of atom coordinates read : 2697 total number of charged atoms : 2549 net assigned charge : 2.500014 assigned positive charge : 407.7948 centred at (gu) : 90.91999 91.37279 96.22958 assigned negative charge : -405.2953 centred at (gu) : 89.59208 90.59257 96.21436 start vw surface at 0.1700000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 196218 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22202 grid for indexing accessible points = 1.400000 m= 104653 mr = 146435 m= 40101 mr = 87671 m= 10160 mr = 32943 m= 1498 mr = 7764 m= 100 mr = 1048 m= 4 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 1.200000 no. cavity mid-points inaccessible to solvent = 3336 time to turn everything in is 1.970000 number of dielectric boundary points 76831 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.130000 number of grid points assigned charge 20388 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) : 1.984466 object centre at (A) : 12.65650 -2.603001 18.64500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1932743 0.1891394 midg,1,midg; midg,igrid,midg -0.1792452 0.3745033 1,midg,midg; igrid,midg,midg -5.4422006E-02 0.6755300 gauss-seidel spectral radius is 0.9992834 estimated iterations to convergence 295 setup time was (sec) 2.300000 now iterating at: 03:54:36 rms-change max change #iterations 10.88594 423.9947 at 10iterations 6.413615 160.1160 at 20iterations 3.768044 73.83326 at 30iterations 2.208599 44.67810 at 40iterations 1.293474 25.55453 at 50iterations 0.7556006 15.35282 at 60iterations 0.4417176 8.405197 at 70iterations 0.2574655 4.454684 at 80iterations 0.1504263 2.545794 at 90iterations 8.7402560E-02 1.553510 at 100iterations 5.0919920E-02 0.9003448 at 110iterations 2.9667621E-02 0.5252342 at 120iterations 1.7287310E-02 0.3023033 at 130iterations 1.0073843E-02 0.1719990 at 140iterations 5.8789030E-03 9.8476410E-02 at 150iterations 3.4528486E-03 5.6959152E-02 at 160iterations 2.0381231E-03 3.4759521E-02 at 170iterations 1.2191718E-03 2.3536682E-02 at 180iterations finished qdiffx linear iterations at : 03:54:50 total time elapsed so far: 16.06000 # loops : 180 mean,max change (kT/e) : 1.2191718E-03 2.3536682E-02 energy calculations done at 16.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.24000 DelPhi exited at 03:54:51 16.242u 0.295s 0:16.98 97.3% 0+0k 0+0io 0pf+0w