Sun Oct 9 13:13:18 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 13:13:18 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2399 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6680678 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): -6.862000 44.10100 ymin,ymax (A): 22.84700 76.13500 zmin,zma (A): 42.15400 85.05400 x,y,z range (A): 50.96300 53.28800 42.90000 scale (grids/A): 0.6680678 object centre (A): 18.61950 49.49100 63.60400 number of atom coordinates read : 2399 total number of charged atoms : 2257 net assigned charge : 2.500025 assigned positive charge : 368.7421 centred at (gu) : 89.64410 90.46538 90.53631 assigned negative charge : -366.2425 centred at (gu) : 89.68544 90.67043 90.59309 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7142 nv = 96 ne = 84 npr = 48327 no. pairs analyzed = 48327 no. exposed pairs = 2900 no. arc points = 20532 no. surface atoms = 979 nbur = 1420 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 458 mr = 3961 m= 3 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.2000000 number of dielectric boundary points 3558 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2024 ## 194 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8394 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8947356E-08 -5.4849547E-09 midg,1,midg; midg,igrid,midg 4.9186742E-08 -4.3892875E-08 1,midg,midg; igrid,midg,midg 1.8990649E-08 -1.1545468E-09 gauss-seidel spectral radius is 0.9883667 estimated iterations to convergence 76 setup time was (sec) 0.3900000 now iterating at: 13:13:18 rms-change max change #iterations 0.1718924 23.39610 at 10iterations 1.8725038E-02 2.401354 at 20iterations 2.1693425E-03 0.3322144 at 30iterations 2.8517537E-04 3.5675049E-02 at 40iterations 5.4681259E-05 8.0204010E-03 at 50iterations finished qdiffx linear iterations at : 13:13:21 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 5.4681259E-05 8.0204010E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 13:13:22 3.397u 0.164s 0:03.83 92.6% 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 13:13:22 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2399 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: 2.004204 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): -6.862000 44.10100 ymin,ymax (A): 22.84700 76.13500 zmin,zma (A): 42.15400 85.05400 x,y,z range (A): 50.96300 53.28800 42.90000 scale (grids/A): 2.004204 object centre (A): 18.61950 49.49100 63.60400 number of atom coordinates read : 2399 total number of charged atoms : 2257 net assigned charge : 2.500025 assigned positive charge : 368.7421 centred at (gu) : 88.93201 91.39572 91.60857 assigned negative charge : -366.2425 centred at (gu) : 89.05614 92.01108 91.77899 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 76717 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20532 grid for indexing accessible points = 1.400000 m= 28667 mr = 53416 m= 4971 mr = 21269 m= 427 mr = 3169 m= 5 mr = 225 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 868 time to turn everything in is 0.3900000 number of dielectric boundary points 32708 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 125 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 17851 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) : 0.6680678 object centre at (A) : 18.61950 49.49100 63.60400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5421986E-02 3.9405799E-03 midg,1,midg; midg,igrid,midg 2.3923926E-02 -5.6751896E-02 1,midg,midg; igrid,midg,midg 3.9400347E-02 -9.6281758E-03 gauss-seidel spectral radius is 0.9987462 estimated iterations to convergence 224 setup time was (sec) 0.6000000 now iterating at: 13:13:22 rms-change max change #iterations 4.544903 210.4453 at 10iterations 2.194266 73.71584 at 20iterations 1.060798 33.76621 at 30iterations 0.5131553 16.92549 at 40iterations 0.2486629 7.521107 at 50iterations 0.1199912 3.712527 at 60iterations 5.7987049E-02 1.848049 at 70iterations 2.8031819E-02 0.8422623 at 80iterations 1.3582903E-02 0.4013557 at 90iterations 6.6082524E-03 0.2038555 at 100iterations 3.2154263E-03 0.1022539 at 110iterations 1.5697664E-03 4.8160911E-02 at 120iterations finished qdiffx linear iterations at : 13:13:29 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 1.5697664E-03 4.8160911E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 13:13:30 7.822u 0.195s 0:08.34 96.0% 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 Sun Oct 9 2011 at 13:13:30 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2399 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: 3.006305 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): -6.862000 44.10100 ymin,ymax (A): 22.84700 76.13500 zmin,zma (A): 42.15400 85.05400 x,y,z range (A): 50.96300 53.28800 42.90000 scale (grids/A): 3.006305 object centre (A): 18.61950 49.49100 63.60400 number of atom coordinates read : 2399 total number of charged atoms : 2257 net assigned charge : 2.500025 assigned positive charge : 368.7421 centred at (gu) : 88.39793 92.09360 92.41271 assigned negative charge : -366.2425 centred at (gu) : 88.58411 93.01664 92.66840 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 177009 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20532 grid for indexing accessible points = 1.400000 m= 91769 mr = 129054 m= 34552 mr = 75360 m= 9200 mr = 28036 m= 1787 mr = 6943 m= 161 mr = 1334 m= 1 mr = 102 m= 0 mr = 0 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 2804 time to turn everything in is 1.000000 number of dielectric boundary points 73650 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 18052 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) : 2.004204 object centre at (A) : 18.61950 49.49100 63.60400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3858073 -2.0517929E-02 midg,1,midg; midg,igrid,midg 0.4783615 -0.6103286 1,midg,midg; igrid,midg,midg 0.3835326 -0.2655776 gauss-seidel spectral radius is 0.9992777 estimated iterations to convergence 294 setup time was (sec) 1.240000 now iterating at: 13:13:31 rms-change max change #iterations 10.42375 451.3636 at 10iterations 6.107628 136.9532 at 20iterations 3.583530 68.99404 at 30iterations 2.096979 41.95075 at 40iterations 1.221173 24.87239 at 50iterations 0.7106295 13.67407 at 60iterations 0.4141833 7.947701 at 70iterations 0.2400564 4.568993 at 80iterations 0.1394897 2.368930 at 90iterations 8.0961861E-02 1.417614 at 100iterations 4.6949491E-02 0.9581108 at 110iterations 2.7291464E-02 0.5532646 at 120iterations 1.5828948E-02 0.2708757 at 130iterations 9.2072999E-03 0.1530342 at 140iterations 5.3589987E-03 9.6277237E-02 at 150iterations 3.1330343E-03 6.5046310E-02 at 160iterations 1.8422144E-03 3.5461426E-02 at 170iterations 1.0956971E-03 2.2300720E-02 at 180iterations finished qdiffx linear iterations at : 13:13:43 total time elapsed so far: 12.56000 # loops : 180 mean,max change (kT/e) : 1.0956971E-03 2.2300720E-02 energy calculations done at 12.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.69000 DelPhi exited at 13:13:43 12.697u 0.201s 0:13.18 97.7% 0+0k 0+0io 0pf+0w