Tue Oct 11 08:29:39 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+sph2.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 = amb2.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 08:29:39 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2836 !!! WARNING: HIR 71 has a net charge of 0.5140 !!! WARNING: SEP 233 has a net charge of -0.4750 !!! WARNING: ASP 287 has a net charge of -0.7280 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: 0.6246710 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): 10.26300 65.04600 ymin,ymax (A): -5.391000 47.54600 zmin,zma (A): -10.00100 46.98900 x,y,z range (A): 54.78300 52.93700 56.99000 scale (grids/A): 0.6246710 object centre (A): 37.65450 21.07750 18.49400 number of atom coordinates read : 2836 total number of charged atoms : 2685 net assigned charge : 4.311021 assigned positive charge : 432.7368 centred at (gu) : 91.73338 90.06892 90.97901 assigned negative charge : -428.4263 centred at (gu) : 91.48586 90.21725 90.98258 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7442 nv = 96 ne = 84 npr = 56735 no. pairs analyzed = 56735 no. exposed pairs = 3478 no. arc points = 24478 no. surface atoms = 1171 nbur = 1665 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 390 mr = 4127 m= 3 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.3700000 number of dielectric boundary points 3651 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2542 ## 282 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9066 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1994842E-09 4.0927954E-09 midg,1,midg; midg,igrid,midg 1.5600740E-08 -9.1311607E-09 1,midg,midg; igrid,midg,midg -1.1984608E-08 3.5016875E-08 gauss-seidel spectral radius is 0.9867488 estimated iterations to convergence 71 setup time was (sec) 0.6400000 now iterating at: 08:29:40 rms-change max change #iterations 0.1394022 27.59249 at 10iterations 1.3331372E-02 1.766014 at 20iterations 1.5378983E-03 0.2008972 at 30iterations 3.0030878E-04 4.6655655E-02 at 40iterations 9.1717229E-05 1.4940262E-02 at 50iterations finished qdiffx linear iterations at : 08:29:43 total time elapsed so far: 3.920000 # loops : 50 mean,max change (kT/e) : 9.1717229E-05 1.4940262E-02 energy calculations done at 3.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.100000 DelPhi exited at 08:29:43 4.106u 0.244s 0:04.66 93.1% 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 08:29:43 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2836 !!! WARNING: HIR 71 has a net charge of 0.5140 !!! WARNING: SEP 233 has a net charge of -0.4750 !!! WARNING: ASP 287 has a net charge of -0.7280 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: 1.874013 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): 10.26300 65.04600 ymin,ymax (A): -5.391000 47.54600 zmin,zma (A): -10.00100 46.98900 x,y,z range (A): 54.78300 52.93700 56.99000 scale (grids/A): 1.874013 object centre (A): 37.65450 21.07750 18.49400 number of atom coordinates read : 2836 total number of charged atoms : 2685 net assigned charge : 4.311021 assigned positive charge : 432.7368 centred at (gu) : 95.20001 90.20662 92.93648 assigned negative charge : -428.4263 centred at (gu) : 94.45751 90.65147 92.94755 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 80045 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24478 grid for indexing accessible points = 1.400000 m= 30136 mr = 55778 m= 4690 mr = 22675 m= 266 mr = 2974 m= 3 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 991 time to turn everything in is 0.7200000 number of dielectric boundary points 33627 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 194 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 21068 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) : 0.6246710 object centre at (A) : 37.65450 21.07750 18.49400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6527425E-02 -1.8639756E-02 midg,1,midg; midg,igrid,midg 2.6853213E-02 -5.0638657E-04 1,midg,midg; igrid,midg,midg -5.2046245E-03 5.4024931E-02 gauss-seidel spectral radius is 0.9986185 estimated iterations to convergence 213 setup time was (sec) 1.010000 now iterating at: 08:29:45 rms-change max change #iterations 4.359456 182.9791 at 10iterations 2.027315 66.29060 at 20iterations 0.9472314 28.77272 at 30iterations 0.4441910 14.06216 at 40iterations 0.2061103 6.810745 at 50iterations 9.6453100E-02 2.800835 at 60iterations 4.5175750E-02 1.364499 at 70iterations 2.1126352E-02 0.6038132 at 80iterations 9.9362656E-03 0.3142719 at 90iterations 4.6763937E-03 0.1503067 at 100iterations 2.2415351E-03 6.7883492E-02 at 110iterations 1.0920301E-03 3.5848618E-02 at 120iterations finished qdiffx linear iterations at : 08:29:53 total time elapsed so far: 9.480000 # loops : 120 mean,max change (kT/e) : 1.0920301E-03 3.5848618E-02 energy calculations done at 9.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.650000 DelPhi exited at 08:29:54 9.657u 0.295s 0:10.48 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 08:29:54 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2836 !!! WARNING: HIR 71 has a net charge of 0.5140 !!! WARNING: SEP 233 has a net charge of -0.4750 !!! WARNING: ASP 287 has a net charge of -0.7280 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: 2.811020 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): 10.26300 65.04600 ymin,ymax (A): -5.391000 47.54600 zmin,zma (A): -10.00100 46.98900 x,y,z range (A): 54.78300 52.93700 56.99000 scale (grids/A): 2.811020 object centre (A): 37.65450 21.07750 18.49400 number of atom coordinates read : 2836 total number of charged atoms : 2685 net assigned charge : 4.311021 assigned positive charge : 432.7368 centred at (gu) : 97.79980 90.30968 94.40457 assigned negative charge : -428.4263 centred at (gu) : 96.68604 90.97707 94.42112 start vw surface at 0.1500000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 185065 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24478 grid for indexing accessible points = 1.400000 m= 96811 mr = 134952 m= 35803 mr = 79840 m= 8415 mr = 29430 m= 1134 mr = 6341 m= 97 mr = 766 m= 0 mr = 42 time to grow re-entrant surface = 1.110000 no. cavity mid-points inaccessible to solvent = 3254 time to turn everything in is 1.840000 number of dielectric boundary points 75954 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 2.000000 number of grid points assigned charge 21478 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) : 1.874013 object centre at (A) : 37.65450 21.07750 18.49400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4222746 -0.3985119 midg,1,midg; midg,igrid,midg 0.2899196 7.8748040E-02 1,midg,midg; igrid,midg,midg -4.0624905E-02 0.5689669 gauss-seidel spectral radius is 0.9992592 estimated iterations to convergence 290 setup time was (sec) 2.180000 now iterating at: 08:29:57 rms-change max change #iterations 10.26926 372.4572 at 10iterations 6.021057 135.4237 at 20iterations 3.510334 79.45532 at 30iterations 2.036087 41.40320 at 40iterations 1.181412 24.71935 at 50iterations 0.6827229 13.58572 at 60iterations 0.3949479 7.227159 at 70iterations 0.2277622 4.114058 at 80iterations 0.1317036 2.426513 at 90iterations 7.5980291E-02 1.448147 at 100iterations 4.3850850E-02 0.8676758 at 110iterations 2.5346871E-02 0.4426920 at 120iterations 1.4698408E-02 0.2745943 at 130iterations 8.5606892E-03 0.1498241 at 140iterations 5.0520962E-03 9.6939087E-02 at 150iterations 3.0333884E-03 6.3096933E-02 at 160iterations 1.8749461E-03 3.3630371E-02 at 170iterations 1.2066700E-03 2.3040771E-02 at 180iterations finished qdiffx linear iterations at : 08:30:11 total time elapsed so far: 16.41000 # loops : 180 mean,max change (kT/e) : 1.2066700E-03 2.3040771E-02 energy calculations done at 16.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.59000 DelPhi exited at 08:30:12 16.591u 0.361s 0:17.62 96.1% 0+0k 0+0io 0pf+0w