Sun Oct 9 22:21:32 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 22:21:32 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3152 !!! WARNING: SEP 140 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6344680 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): -5.325000 47.61700 ymin,ymax (A): 39.57200 94.07200 zmin,zma (A): 3.361000 59.47100 x,y,z range (A): 52.94200 54.50000 56.11000 scale (grids/A): 0.6344680 object centre (A): 21.14600 66.82200 31.41600 number of atom coordinates read : 3152 total number of charged atoms : 3003 net assigned charge : 5.025017 assigned positive charge : 479.8628 centred at (gu) : 89.50150 90.11121 88.71621 assigned negative charge : -474.8391 centred at (gu) : 89.48838 90.19144 88.62609 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8589 nv = 96 ne = 84 npr = 61610 no. pairs analyzed = 61610 no. exposed pairs = 4099 no. arc points = 29449 no. surface atoms = 1376 nbur = 1776 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 493 mr = 4544 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 46 time to turn everything in is 0.4100000 number of dielectric boundary points 4498 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2907 ## 271 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 10405 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.4112977E-09 1.3165748E-08 midg,1,midg; midg,igrid,midg 1.5759476E-08 -3.5882390E-09 1,midg,midg; igrid,midg,midg 5.3212958E-09 7.2160078E-09 gauss-seidel spectral radius is 0.9871904 estimated iterations to convergence 72 setup time was (sec) 0.6800000 now iterating at: 22:21:32 rms-change max change #iterations 0.1599618 26.14831 at 10iterations 1.5178611E-02 2.300667 at 20iterations 1.5090241E-03 0.2234306 at 30iterations 1.4642393E-04 2.3112535E-02 at 40iterations 1.5417767E-05 1.8005371E-03 at 50iterations finished qdiffx linear iterations at : 22:21:36 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 1.5417767E-05 1.8005371E-03 energy calculations done at 3.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.140000 DelPhi exited at 22:21:36 4.140u 0.244s 0:04.65 94.1% 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 Sun Oct 9 2011 at 22:21:36 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3152 !!! WARNING: SEP 140 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.903404 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): -5.325000 47.61700 ymin,ymax (A): 39.57200 94.07200 zmin,zma (A): 3.361000 59.47100 x,y,z range (A): 52.94200 54.50000 56.11000 scale (grids/A): 1.903404 object centre (A): 21.14600 66.82200 31.41600 number of atom coordinates read : 3152 total number of charged atoms : 3003 net assigned charge : 5.025017 assigned positive charge : 479.8628 centred at (gu) : 88.50375 90.33305 86.14810 assigned negative charge : -474.8391 centred at (gu) : 88.46485 90.57375 85.87784 start vw surface at 0.1700000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 93010 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29449 grid for indexing accessible points = 1.400000 m= 31862 mr = 63037 m= 4899 mr = 22539 m= 301 mr = 2844 m= 4 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 2280 time to turn everything in is 0.8100000 number of dielectric boundary points 41564 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 194 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 23595 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) : 0.6344680 object centre at (A) : 21.14600 66.82200 31.41600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3164285E-02 2.6881933E-02 midg,1,midg; midg,igrid,midg 1.4824594E-02 2.0004241E-04 1,midg,midg; igrid,midg,midg -5.4921941E-03 1.0493024E-03 gauss-seidel spectral radius is 0.9987013 estimated iterations to convergence 220 setup time was (sec) 1.100000 now iterating at: 22:21:38 rms-change max change #iterations 4.712626 190.4499 at 10iterations 2.241477 66.76437 at 20iterations 1.069176 31.30674 at 30iterations 0.5075436 15.27415 at 40iterations 0.2424263 6.868984 at 50iterations 0.1153493 3.893559 at 60iterations 5.4791387E-02 1.778692 at 70iterations 2.6166422E-02 0.7970316 at 80iterations 1.2460642E-02 0.3398476 at 90iterations 5.9202253E-03 0.1745024 at 100iterations 2.8365813E-03 8.3866119E-02 at 110iterations 1.3513829E-03 3.9883137E-02 at 120iterations finished qdiffx linear iterations at : 22:21:46 total time elapsed so far: 9.530000 # loops : 120 mean,max change (kT/e) : 1.3513829E-03 3.9883137E-02 energy calculations done at 9.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.710000 DelPhi exited at 22:21:47 9.709u 0.299s 0:10.38 96.2% 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 22:21:47 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3152 !!! WARNING: SEP 140 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.855106 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): -5.325000 47.61700 ymin,ymax (A): 39.57200 94.07200 zmin,zma (A): 3.361000 59.47100 x,y,z range (A): 52.94200 54.50000 56.11000 scale (grids/A): 2.855106 object centre (A): 21.14600 66.82200 31.41600 number of atom coordinates read : 3152 total number of charged atoms : 3003 net assigned charge : 5.025017 assigned positive charge : 479.8628 centred at (gu) : 87.75548 90.49921 84.22187 assigned negative charge : -474.8391 centred at (gu) : 87.69717 90.86070 83.81663 start vw surface at 0.1700000 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 215099 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29449 grid for indexing accessible points = 1.400000 m= 104039 mr = 153110 m= 36031 mr = 83410 m= 8470 mr = 27773 m= 1223 mr = 6071 m= 90 mr = 759 m= 1 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 1.260000 no. cavity mid-points inaccessible to solvent = 7482 time to turn everything in is 2.060000 number of dielectric boundary points 93776 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.230000 number of grid points assigned charge 24022 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) : 1.903404 object centre at (A) : 21.14600 66.82200 31.41600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3589703 0.2165859 midg,1,midg; midg,igrid,midg 0.2618085 0.1260186 1,midg,midg; igrid,midg,midg -0.2457713 3.7636146E-02 gauss-seidel spectral radius is 0.9992965 estimated iterations to convergence 297 setup time was (sec) 2.400000 now iterating at: 22:21:49 rms-change max change #iterations 11.25962 345.2266 at 10iterations 6.741177 157.0633 at 20iterations 4.004066 86.64176 at 30iterations 2.374465 52.99077 at 40iterations 1.398432 27.79434 at 50iterations 0.8239578 16.61904 at 60iterations 0.4837980 8.653035 at 70iterations 0.2841538 5.249075 at 80iterations 0.1665252 2.724618 at 90iterations 9.7241998E-02 1.755529 at 100iterations 5.6989700E-02 1.030782 at 110iterations 3.3291183E-02 0.5377078 at 120iterations 1.9450285E-02 0.3077307 at 130iterations 1.1362854E-02 0.1893344 at 140iterations 6.6353404E-03 0.1167686 at 150iterations 3.8666176E-03 6.1674595E-02 at 160iterations 2.2615748E-03 3.6816597E-02 at 170iterations 1.3187885E-03 2.1232605E-02 at 180iterations finished qdiffx linear iterations at : 22:22:04 total time elapsed so far: 16.55000 # loops : 180 mean,max change (kT/e) : 1.3187885E-03 2.1232605E-02 energy calculations done at 16.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.73000 DelPhi exited at 22:22:04 16.730u 0.321s 0:17.32 98.4% 0+0k 0+0io 0pf+0w