Tue Oct 11 07:54:57 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 07:54:57 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 = 2366 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: 0.6384505 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): -24.61200 21.35800 ymin,ymax (A): 4.105000 59.86500 zmin,zma (A): -20.16200 24.79100 x,y,z range (A): 45.97000 55.76000 44.95300 scale (grids/A): 0.6384505 object centre (A): -1.627000 31.98500 2.314501 number of atom coordinates read : 2366 total number of charged atoms : 2241 net assigned charge : 5.500007 assigned positive charge : 356.6153 centred at (gu) : 90.59368 91.12523 89.32791 assigned negative charge : -351.1158 centred at (gu) : 90.40472 91.16570 89.37621 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6375 nv = 96 ne = 84 npr = 48572 no. pairs analyzed = 48572 no. exposed pairs = 2873 no. arc points = 20174 no. surface atoms = 967 nbur = 1399 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 312 mr = 3503 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3154 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2017 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7673 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4308522E-08 2.3402276E-09 midg,1,midg; midg,igrid,midg 9.1811891E-09 4.2847246E-09 1,midg,midg; igrid,midg,midg -1.0434123E-08 2.9839061E-08 gauss-seidel spectral radius is 0.9872662 estimated iterations to convergence 72 setup time was (sec) 0.5000000 now iterating at: 07:54:58 rms-change max change #iterations 0.1359598 19.77127 at 10iterations 1.3234584E-02 1.849029 at 20iterations 1.3101876E-03 0.1843505 at 30iterations 1.2721433E-04 1.9366980E-02 at 40iterations 1.2806810E-05 2.0599365E-03 at 50iterations finished qdiffx linear iterations at : 07:55:01 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 1.2806810E-05 2.0599365E-03 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.100000 DelPhi exited at 07:55:01 3.107u 0.135s 0:03.56 90.7% 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 07:55:01 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 = 2366 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: 1.915351 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): -24.61200 21.35800 ymin,ymax (A): 4.105000 59.86500 zmin,zma (A): -20.16200 24.79100 x,y,z range (A): 45.97000 55.76000 44.95300 scale (grids/A): 1.915351 object centre (A): -1.627000 31.98500 2.314501 number of atom coordinates read : 2366 total number of charged atoms : 2241 net assigned charge : 5.500007 assigned positive charge : 356.6153 centred at (gu) : 91.78088 93.37548 87.98326 assigned negative charge : -351.1158 centred at (gu) : 91.21423 93.49690 88.12854 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 68251 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20174 grid for indexing accessible points = 1.400000 m= 24234 mr = 47077 m= 3714 mr = 17884 m= 180 mr = 2223 m= 3 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 485 time to turn everything in is 0.4800000 number of dielectric boundary points 29143 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 174 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 17643 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) : 0.6384505 object centre at (A) : -1.627000 31.98500 2.314501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9396264E-02 1.2391968E-02 midg,1,midg; midg,igrid,midg 4.7429066E-02 1.4830040E-02 1,midg,midg; igrid,midg,midg -8.7577440E-03 2.2817211E-02 gauss-seidel spectral radius is 0.9986249 estimated iterations to convergence 214 setup time was (sec) 0.7500000 now iterating at: 07:55:02 rms-change max change #iterations 4.055460 201.7455 at 10iterations 1.902247 67.77618 at 20iterations 0.8860534 30.39369 at 30iterations 0.4127417 13.42593 at 40iterations 0.1942680 6.101257 at 50iterations 9.0610109E-02 2.806557 at 60iterations 4.2299528E-02 1.495078 at 70iterations 1.9806346E-02 0.6979842 at 80iterations 9.2202863E-03 0.3361778 at 90iterations 4.3029976E-03 0.1493225 at 100iterations 2.0097094E-03 6.7907572E-02 at 110iterations 9.4170903E-04 2.9252052E-02 at 120iterations finished qdiffx linear iterations at : 07:55:08 total time elapsed so far: 7.100000 # loops : 120 mean,max change (kT/e) : 9.4170903E-04 2.9252052E-02 energy calculations done at 7.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.290000 DelPhi exited at 07:55:09 7.290u 0.157s 0:07.86 94.6% 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 Tue Oct 11 2011 at 07:55:09 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 = 2366 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: 2.873027 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): -24.61200 21.35800 ymin,ymax (A): 4.105000 59.86500 zmin,zma (A): -20.16200 24.79100 x,y,z range (A): 45.97000 55.76000 44.95300 scale (grids/A): 2.873027 object centre (A): -1.627000 31.98500 2.314501 number of atom coordinates read : 2366 total number of charged atoms : 2241 net assigned charge : 5.500007 assigned positive charge : 356.6153 centred at (gu) : 92.67130 95.06303 86.97486 assigned negative charge : -351.1158 centred at (gu) : 91.82133 95.24523 87.19272 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 157586 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20174 grid for indexing accessible points = 1.400000 m= 79207 mr = 114022 m= 28155 mr = 64722 m= 6746 mr = 22682 m= 885 mr = 4982 m= 39 mr = 551 m= 0 mr = 20 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 1579 time to turn everything in is 1.190000 number of dielectric boundary points 65639 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 17926 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) : 1.915351 object centre at (A) : -1.627000 31.98500 2.314501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2034044 0.1543552 midg,1,midg; midg,igrid,midg 0.5906433 6.6150077E-02 1,midg,midg; igrid,midg,midg -4.6188224E-02 0.1541179 gauss-seidel spectral radius is 0.9992471 estimated iterations to convergence 288 setup time was (sec) 1.470000 now iterating at: 07:55:11 rms-change max change #iterations 9.444822 362.8019 at 10iterations 5.454893 144.0106 at 20iterations 3.140090 98.42384 at 30iterations 1.805484 40.76094 at 40iterations 1.034420 22.32220 at 50iterations 0.5927240 11.33380 at 60iterations 0.3395306 6.152643 at 70iterations 0.1941931 4.134070 at 80iterations 0.1110917 2.084244 at 90iterations 6.3465506E-02 1.244209 at 100iterations 3.6281716E-02 0.6814216 at 110iterations 2.0752495E-02 0.3891098 at 120iterations 1.1838090E-02 0.2343483 at 130iterations 6.7794826E-03 0.1241531 at 140iterations 3.8822014E-03 7.3036194E-02 at 150iterations 2.2170690E-03 4.1419983E-02 at 160iterations 1.2644677E-03 2.3818970E-02 at 170iterations 7.2453270E-04 1.2901306E-02 at 180iterations finished qdiffx linear iterations at : 07:55:20 total time elapsed so far: 11.27000 # loops : 180 mean,max change (kT/e) : 7.2453270E-04 1.2901306E-02 energy calculations done at 11.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.48000 DelPhi exited at 07:55:21 11.482u 0.161s 0:11.95 97.4% 0+0k 0+0io 0pf+0w