Tue Oct 11 03:49:02 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 03:49:03 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 = 2703 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6604946 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): -11.77200 37.08900 ymin,ymax (A): -25.99000 22.28900 zmin,zma (A): -8.441999 45.45700 x,y,z range (A): 48.86100 48.27900 53.89900 scale (grids/A): 0.6604946 object centre (A): 12.65850 -1.850500 18.50750 number of atom coordinates read : 2703 total number of charged atoms : 2555 net assigned charge : 4.500012 assigned positive charge : 408.4558 centred at (gu) : 90.27985 90.28598 91.44129 assigned negative charge : -403.9563 centred at (gu) : 90.04172 90.12582 91.42309 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7865 nv = 96 ne = 84 npr = 55809 no. pairs analyzed = 55809 no. exposed pairs = 3324 no. arc points = 23252 no. surface atoms = 1108 nbur = 1595 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 450 mr = 4410 m= 2 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.3900000 number of dielectric boundary points 3856 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2274 ## 208 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 9365 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.7152332E-09 2.0322611E-08 midg,1,midg; midg,igrid,midg -2.1213186E-08 4.6851010E-08 1,midg,midg; igrid,midg,midg -3.7199182E-08 6.3304050E-08 gauss-seidel spectral radius is 0.9881261 estimated iterations to convergence 75 setup time was (sec) 0.6800000 now iterating at: 03:49:03 rms-change max change #iterations 0.1712448 20.89432 at 10iterations 1.8766563E-02 2.392874 at 20iterations 2.0638155E-03 0.2787175 at 30iterations 2.6943884E-04 3.7694931E-02 at 40iterations 5.0975865E-05 7.5073242E-03 at 50iterations finished qdiffx linear iterations at : 03:49:07 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 5.0975865E-05 7.5073242E-03 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 03:49:07 4.241u 0.238s 0:04.87 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 03:49:08 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 = 2703 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.981484 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): -11.77200 37.08900 ymin,ymax (A): -25.99000 22.28900 zmin,zma (A): -8.441999 45.45700 x,y,z range (A): 48.86100 48.27900 53.89900 scale (grids/A): 1.981484 object centre (A): 12.65850 -1.850500 18.50750 number of atom coordinates read : 2703 total number of charged atoms : 2555 net assigned charge : 4.500012 assigned positive charge : 408.4558 centred at (gu) : 90.83865 90.85758 94.32335 assigned negative charge : -403.9563 centred at (gu) : 90.12482 90.37712 94.26892 start vw surface at 0.2000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 84748 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23252 grid for indexing accessible points = 1.400000 m= 31259 mr = 59612 m= 5073 mr = 23173 m= 337 mr = 3156 m= 5 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 484 time to turn everything in is 0.7900000 number of dielectric boundary points 35365 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 152 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 20181 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) : 0.6604946 object centre at (A) : 12.65850 -1.850500 18.50750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5509396E-02 1.1800999E-02 midg,1,midg; midg,igrid,midg -1.3040400E-02 3.3586964E-02 1,midg,midg; igrid,midg,midg -9.1994889E-03 7.2491549E-02 gauss-seidel spectral radius is 0.9987456 estimated iterations to convergence 224 setup time was (sec) 1.150000 now iterating at: 03:49:09 rms-change max change #iterations 4.664932 191.9192 at 10iterations 2.269616 66.45822 at 20iterations 1.097268 33.57510 at 30iterations 0.5293033 18.56701 at 40iterations 0.2572263 7.763153 at 50iterations 0.1243267 3.760746 at 60iterations 6.0182046E-02 1.804194 at 70iterations 2.9148739E-02 0.8473740 at 80iterations 1.4127474E-02 0.4322815 at 90iterations 6.8804570E-03 0.1981201 at 100iterations 3.3560251E-03 9.1459274E-02 at 110iterations 1.6408555E-03 4.7254562E-02 at 120iterations finished qdiffx linear iterations at : 03:49:17 total time elapsed so far: 9.390000 # loops : 120 mean,max change (kT/e) : 1.6408555E-03 4.7254562E-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) 9.620000 DelPhi exited at 03:49:18 9.623u 0.247s 0:10.48 94.0% 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 03:49:18 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 = 2703 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.972226 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): -11.77200 37.08900 ymin,ymax (A): -25.99000 22.28900 zmin,zma (A): -8.441999 45.45700 x,y,z range (A): 48.86100 48.27900 53.89900 scale (grids/A): 2.972226 object centre (A): 12.65850 -1.850500 18.50750 number of atom coordinates read : 2703 total number of charged atoms : 2555 net assigned charge : 4.500012 assigned positive charge : 408.4558 centred at (gu) : 91.25793 91.28622 96.48481 assigned negative charge : -403.9563 centred at (gu) : 90.18719 90.56562 96.40321 start vw surface at 0.2100000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 195670 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23252 grid for indexing accessible points = 1.400000 m= 100934 mr = 144048 m= 36947 mr = 83117 m= 9178 mr = 29509 m= 1376 mr = 6817 m= 94 mr = 930 m= 0 mr = 33 time to grow re-entrant surface = 1.190000 no. cavity mid-points inaccessible to solvent = 1673 time to turn everything in is 2.010000 number of dielectric boundary points 79745 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.180000 number of grid points assigned charge 20440 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) : 1.981484 object centre at (A) : 12.65850 -1.850500 18.50750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3949862 0.2802872 midg,1,midg; midg,igrid,midg -0.1620024 0.3803793 1,midg,midg; igrid,midg,midg -5.7553697E-02 0.5930357 gauss-seidel spectral radius is 0.9992853 estimated iterations to convergence 295 setup time was (sec) 2.380000 now iterating at: 03:49:21 rms-change max change #iterations 10.74304 358.8106 at 10iterations 6.314425 158.0404 at 20iterations 3.705457 73.68388 at 30iterations 2.168430 45.15791 at 40iterations 1.265922 31.42924 at 50iterations 0.7416676 13.60769 at 60iterations 0.4320326 7.183495 at 70iterations 0.2522793 4.660362 at 80iterations 0.1466037 2.694607 at 90iterations 8.5478358E-02 1.560944 at 100iterations 4.9826123E-02 0.8628464 at 110iterations 2.9029706E-02 0.5997045 at 120iterations 1.6888203E-02 0.2839832 at 130iterations 9.8887151E-03 0.1616590 at 140iterations 5.7800128E-03 9.8209381E-02 at 150iterations 3.4043100E-03 5.8654785E-02 at 160iterations 2.0257025E-03 3.5253525E-02 at 170iterations 1.2192291E-03 2.2552490E-02 at 180iterations finished qdiffx linear iterations at : 03:49:33 total time elapsed so far: 14.97000 # loops : 180 mean,max change (kT/e) : 1.2192291E-03 2.2552490E-02 energy calculations done at 14.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.25000 DelPhi exited at 03:49:34 15.251u 0.309s 0:15.96 97.4% 0+0k 0+0io 0pf+0w