Tue Oct 11 03:26:53 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 03:26:53 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 = 2244 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5988124 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): -26.25200 23.89500 ymin,ymax (A): -22.68700 21.57200 zmin,zma (A): -34.60600 24.84500 x,y,z range (A): 50.14700 44.25900 59.45100 scale (grids/A): 0.5988124 object centre (A): -1.178499 -0.5574999 -4.880501 number of atom coordinates read : 2244 total number of charged atoms : 2101 net assigned charge : 3.000010 assigned positive charge : 328.5804 centred at (gu) : 91.49189 89.47977 91.62695 assigned negative charge : -325.5810 centred at (gu) : 91.56907 89.56729 91.47735 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 5490 nv = 96 ne = 84 npr = 44093 no. pairs analyzed = 44093 no. exposed pairs = 3025 no. arc points = 21795 no. surface atoms = 1012 nbur = 1232 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 269 mr = 2746 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.1600000 number of dielectric boundary points 2991 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2146 ## 234 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6707 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2477920E-09 8.0009688E-09 midg,1,midg; midg,igrid,midg 4.1896917E-09 -1.2496555E-09 1,midg,midg; igrid,midg,midg 2.4453564E-09 -1.6012840E-09 gauss-seidel spectral radius is 0.9855459 estimated iterations to convergence 68 setup time was (sec) 0.3500000 now iterating at: 03:26:54 rms-change max change #iterations 9.8352700E-02 16.02181 at 10iterations 8.3090607E-03 1.312710 at 20iterations 7.0315640E-04 0.1056194 at 30iterations 5.8137859E-05 1.0911942E-02 at 40iterations 4.7792992E-06 7.8201294E-04 at 50iterations finished qdiffx linear iterations at : 03:26:57 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 4.7792992E-06 7.8201294E-04 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 03:26:57 3.349u 0.176s 0:03.92 89.5% 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 03:26:57 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 = 2244 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.796437 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): -26.25200 23.89500 ymin,ymax (A): -22.68700 21.57200 zmin,zma (A): -34.60600 24.84500 x,y,z range (A): 50.14700 44.25900 59.45100 scale (grids/A): 1.796437 object centre (A): -1.178499 -0.5574999 -4.880501 number of atom coordinates read : 2244 total number of charged atoms : 2101 net assigned charge : 3.000010 assigned positive charge : 328.5804 centred at (gu) : 94.47529 88.43871 94.88059 assigned negative charge : -325.5810 centred at (gu) : 94.70734 88.70180 94.43203 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 59258 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21795 grid for indexing accessible points = 1.400000 m= 19861 mr = 38803 m= 2635 mr = 13930 m= 129 mr = 1424 m= 2 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 113 time to turn everything in is 0.3000000 number of dielectric boundary points 27701 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 178 iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 16393 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) : 0.5988124 object centre at (A) : -1.178499 -0.5574999 -4.880501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6397014E-02 1.5523329E-02 midg,1,midg; midg,igrid,midg 1.1578074E-02 -3.7864258E-03 1,midg,midg; igrid,midg,midg 9.4036032E-03 1.7027296E-03 gauss-seidel spectral radius is 0.9984376 estimated iterations to convergence 201 setup time was (sec) 0.5100000 now iterating at: 03:26:58 rms-change max change #iterations 3.423114 184.7901 at 10iterations 1.511599 62.25517 at 20iterations 0.6719721 22.94922 at 30iterations 0.2974531 11.37792 at 40iterations 0.1320469 5.240479 at 50iterations 5.8684997E-02 2.067664 at 60iterations 2.5949074E-02 0.8991528 at 70iterations 1.1525054E-02 0.4550591 at 80iterations 5.1200907E-03 0.2272453 at 90iterations 2.2707246E-03 8.2320213E-02 at 100iterations 1.0103381E-03 3.7906647E-02 at 110iterations 4.4851648E-04 1.7027855E-02 at 120iterations finished qdiffx linear iterations at : 03:27:05 total time elapsed so far: 7.520000 # loops : 120 mean,max change (kT/e) : 4.4851648E-04 1.7027855E-02 energy calculations done at 7.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 03:27:06 7.654u 0.192s 0:08.20 95.6% 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 03:27:06 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 = 2244 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.694656 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): -26.25200 23.89500 ymin,ymax (A): -22.68700 21.57200 zmin,zma (A): -34.60600 24.84500 x,y,z range (A): 50.14700 44.25900 59.45100 scale (grids/A): 2.694656 object centre (A): -1.178499 -0.5574999 -4.880501 number of atom coordinates read : 2244 total number of charged atoms : 2101 net assigned charge : 3.000010 assigned positive charge : 328.5804 centred at (gu) : 96.71291 87.65797 97.32076 assigned negative charge : -325.5810 centred at (gu) : 97.06113 88.05273 96.64804 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 136906 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21795 grid for indexing accessible points = 1.400000 m= 65136 mr = 94583 m= 22019 mr = 51612 m= 4506 mr = 17096 m= 474 mr = 3006 m= 24 mr = 280 m= 0 mr = 6 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 463 time to turn everything in is 0.7300000 number of dielectric boundary points 62482 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 16808 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) : 1.796437 object centre at (A) : -1.178499 -0.5574999 -4.880501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.8576975E-02 0.1768801 midg,1,midg; midg,igrid,midg 0.1246328 -3.5848398E-02 1,midg,midg; igrid,midg,midg 9.2675105E-02 4.7249044E-03 gauss-seidel spectral radius is 0.9992076 estimated iterations to convergence 280 setup time was (sec) 0.9700000 now iterating at: 03:27:07 rms-change max change #iterations 8.451824 333.5569 at 10iterations 4.878911 131.6921 at 20iterations 2.781717 61.92485 at 30iterations 1.582850 39.65393 at 40iterations 0.8980128 21.45850 at 50iterations 0.5092344 12.78606 at 60iterations 0.2879557 6.046656 at 70iterations 0.1623757 3.772821 at 80iterations 9.1624483E-02 2.064484 at 90iterations 5.1777657E-02 1.348267 at 100iterations 2.9230405E-02 0.7143631 at 110iterations 1.6424211E-02 0.3519058 at 120iterations 9.2751989E-03 0.1948757 at 130iterations 5.2281292E-03 0.1111088 at 140iterations 2.9390599E-03 6.3545227E-02 at 150iterations 1.6525651E-03 3.6628723E-02 at 160iterations 9.3521504E-04 1.9996643E-02 at 170iterations 5.2854017E-04 1.1374474E-02 at 180iterations finished qdiffx linear iterations at : 03:27:18 total time elapsed so far: 12.08000 # loops : 180 mean,max change (kT/e) : 5.2854017E-04 1.1374474E-02 energy calculations done at 12.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.21000 DelPhi exited at 03:27:18 12.214u 0.203s 0:12.76 97.2% 0+0k 0+0io 0pf+0w