Sun Oct 9 07:11:22 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 Sun Oct 9 2011 at 07:11:23 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2004 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6580042 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): -13.18200 38.74300 ymin,ymax (A): -22.30600 29.48500 zmin,zma (A): -15.41600 38.68700 x,y,z range (A): 51.92500 51.79100 54.10300 scale (grids/A): 0.6580042 object centre (A): 12.78050 3.589499 11.63550 number of atom coordinates read : 2004 total number of charged atoms : 1819 net assigned charge : 3.000006 assigned positive charge : 288.5011 centred at (gu) : 90.26862 90.28796 89.22591 assigned negative charge : -285.5012 centred at (gu) : 90.38146 90.20940 89.02743 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5852 nv = 96 ne = 84 npr = 41674 no. pairs analyzed = 41674 no. exposed pairs = 2501 no. arc points = 17958 no. surface atoms = 848 nbur = 1156 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 301 mr = 3128 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.2300000 number of dielectric boundary points 3009 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1731 ## 150 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 6653 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4277002E-08 2.9231780E-08 midg,1,midg; midg,igrid,midg -3.2022656E-09 1.9415316E-08 1,midg,midg; igrid,midg,midg 2.1674886E-08 -8.7777563E-09 gauss-seidel spectral radius is 0.9879778 estimated iterations to convergence 74 setup time was (sec) 0.4500000 now iterating at: 07:11:23 rms-change max change #iterations 0.1392049 21.64408 at 10iterations 1.4596578E-02 2.360517 at 20iterations 1.5330822E-03 0.2641602 at 30iterations 1.6055797E-04 2.4753571E-02 at 40iterations 1.7065691E-05 2.9459000E-03 at 50iterations finished qdiffx linear iterations at : 07:11:25 total time elapsed so far: 2.860000 # loops : 50 mean,max change (kT/e) : 1.7065691E-05 2.9459000E-03 energy calculations done at 2.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.030000 DelPhi exited at 07:11:26 3.038u 0.158s 0:03.47 91.6% 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 Sun Oct 9 2011 at 07:11:26 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2004 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.974012 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): -13.18200 38.74300 ymin,ymax (A): -22.30600 29.48500 zmin,zma (A): -15.41600 38.68700 x,y,z range (A): 51.92500 51.79100 54.10300 scale (grids/A): 1.974012 object centre (A): 12.78050 3.589499 11.63550 number of atom coordinates read : 2004 total number of charged atoms : 1819 net assigned charge : 3.000006 assigned positive charge : 288.5011 centred at (gu) : 90.80598 90.86353 87.67753 assigned negative charge : -285.5012 centred at (gu) : 91.14462 90.62823 87.08234 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 62219 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17958 grid for indexing accessible points = 1.400000 m= 22772 mr = 42112 m= 3591 mr = 16841 m= 192 mr = 2202 m= 1 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 521 time to turn everything in is 0.4600000 number of dielectric boundary points 27539 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 106 iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 14355 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) : 0.6580042 object centre at (A) : 12.78050 3.589499 11.63550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.3097710E-02 2.4488322E-02 midg,1,midg; midg,igrid,midg 1.3514534E-02 4.2085148E-02 1,midg,midg; igrid,midg,midg 1.7015744E-02 -2.6376911E-02 gauss-seidel spectral radius is 0.9986706 estimated iterations to convergence 217 setup time was (sec) 0.7300000 now iterating at: 07:11:27 rms-change max change #iterations 3.853636 163.4706 at 10iterations 1.826349 68.89722 at 20iterations 0.8611974 28.95622 at 30iterations 0.4055393 12.96823 at 40iterations 0.1925746 6.682053 at 50iterations 9.0430260E-02 3.019096 at 60iterations 4.2728394E-02 1.558886 at 70iterations 2.0282382E-02 0.6405163 at 80iterations 9.5574148E-03 0.3071861 at 90iterations 4.5293057E-03 0.1550217 at 100iterations 2.1487584E-03 8.5073113E-02 at 110iterations 1.0132719E-03 3.4790039E-02 at 120iterations finished qdiffx linear iterations at : 07:11:33 total time elapsed so far: 6.620000 # loops : 120 mean,max change (kT/e) : 1.0132719E-03 3.4790039E-02 energy calculations done at 6.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.800000 DelPhi exited at 07:11:33 6.802u 0.155s 0:07.25 95.8% 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 Sun Oct 9 2011 at 07:11:33 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2004 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: 2.961019 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): -13.18200 38.74300 ymin,ymax (A): -22.30600 29.48500 zmin,zma (A): -15.41600 38.68700 x,y,z range (A): 51.92500 51.79100 54.10300 scale (grids/A): 2.961019 object centre (A): 12.78050 3.589499 11.63550 number of atom coordinates read : 2004 total number of charged atoms : 1819 net assigned charge : 3.000006 assigned positive charge : 288.5011 centred at (gu) : 91.20894 91.29548 86.51640 assigned negative charge : -285.5012 centred at (gu) : 91.71693 90.94231 85.62349 start vw surface at 0.1300000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 143525 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17958 grid for indexing accessible points = 1.400000 m= 73111 mr = 102087 m= 27068 mr = 59920 m= 6349 mr = 21675 m= 867 mr = 4620 m= 54 mr = 562 m= 0 mr = 34 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 1683 time to turn everything in is 1.110000 number of dielectric boundary points 62076 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 14552 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) : 1.974012 object centre at (A) : 12.78050 3.589499 11.63550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5971895 0.2368444 midg,1,midg; midg,igrid,midg 0.2067721 0.4681781 1,midg,midg; igrid,midg,midg 0.2837940 -0.2025618 gauss-seidel spectral radius is 0.9992585 estimated iterations to convergence 290 setup time was (sec) 1.390000 now iterating at: 07:11:35 rms-change max change #iterations 8.842203 427.1875 at 10iterations 5.096248 113.3965 at 20iterations 2.927159 61.52215 at 30iterations 1.684282 32.23754 at 40iterations 0.9661806 20.97691 at 50iterations 0.5551606 10.63235 at 60iterations 0.3174993 7.299293 at 70iterations 0.1817872 3.362282 at 80iterations 0.1044700 2.062408 at 90iterations 5.9863571E-02 1.325070 at 100iterations 3.4325298E-02 0.6736231 at 110iterations 1.9694924E-02 0.3934212 at 120iterations 1.1265029E-02 0.2469120 at 130iterations 6.4673433E-03 0.1340036 at 140iterations 3.7120096E-03 6.8683624E-02 at 150iterations 2.1275475E-03 4.2560190E-02 at 160iterations 1.2171080E-03 2.4559021E-02 at 170iterations 6.9836393E-04 1.4869690E-02 at 180iterations finished qdiffx linear iterations at : 07:11:44 total time elapsed so far: 10.74000 # loops : 180 mean,max change (kT/e) : 6.9836393E-04 1.4869690E-02 energy calculations done at 10.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.92000 DelPhi exited at 07:11:45 10.919u 0.173s 0:11.37 97.4% 0+0k 0+0io 0pf+0w