Tue Oct 11 05:27:20 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 05:27:20 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 = 1986 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: 0.7302714 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): -3.891000 44.85800 ymin,ymax (A): -22.31200 24.40800 zmin,zma (A): 5.566000 48.21200 x,y,z range (A): 48.74900 46.72000 42.64600 scale (grids/A): 0.7302714 object centre (A): 20.48350 1.048000 26.88900 number of atom coordinates read : 1986 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.2470 centred at (gu) : 91.02042 89.23690 89.67272 assigned negative charge : -303.7472 centred at (gu) : 90.89963 89.36768 89.60262 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7500 nv = 96 ne = 84 npr = 37723 no. pairs analyzed = 37723 no. exposed pairs = 2570 no. arc points = 17639 no. surface atoms = 869 nbur = 1117 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 561 mr = 4281 m= 3 mr = 134 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3649 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1607 ## 144 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8062 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2220830E-08 1.5044461E-07 midg,1,midg; midg,igrid,midg 2.3882419E-07 1.4298446E-09 1,midg,midg; igrid,midg,midg 8.2433989E-09 2.4143711E-07 gauss-seidel spectral radius is 0.9902163 estimated iterations to convergence 82 setup time was (sec) 0.5600000 now iterating at: 05:27:21 rms-change max change #iterations 0.2243364 32.27025 at 10iterations 2.9362453E-02 4.298276 at 20iterations 3.9501530E-03 0.5575218 at 30iterations 5.7830632E-04 8.1433296E-02 at 40iterations 1.1243823E-04 1.6954422E-02 at 50iterations finished qdiffx linear iterations at : 05:27:24 total time elapsed so far: 3.890000 # loops : 50 mean,max change (kT/e) : 1.1243823E-04 1.6954422E-02 energy calculations done at 3.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.070000 DelPhi exited at 05:27:25 4.071u 0.277s 0:04.84 89.6% 0+0k 0+0io 7pf+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 05:27:25 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 = 1986 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: 2.190814 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): -3.891000 44.85800 ymin,ymax (A): -22.31200 24.40800 zmin,zma (A): 5.566000 48.21200 x,y,z range (A): 48.74900 46.72000 42.64600 scale (grids/A): 2.190814 object centre (A): 20.48350 1.048000 26.88900 number of atom coordinates read : 1986 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.2470 centred at (gu) : 93.06123 87.71117 89.01814 assigned negative charge : -303.7472 centred at (gu) : 92.69892 88.10321 88.80814 start vw surface at 0.1200000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 78970 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17639 grid for indexing accessible points = 1.400000 m= 33638 mr = 55767 m= 6995 mr = 25756 m= 719 mr = 4784 m= 26 mr = 394 m= 0 mr = 2 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7200000 number of dielectric boundary points 33645 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 60 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 15332 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) : 0.7302714 object centre at (A) : 20.48350 1.048000 26.88900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8914381E-02 3.0102367E-02 midg,1,midg; midg,igrid,midg 4.9479794E-02 -4.7118071E-02 1,midg,midg; igrid,midg,midg 4.6476789E-02 0.1065666 gauss-seidel spectral radius is 0.9988902 estimated iterations to convergence 238 setup time was (sec) 1.020000 now iterating at: 05:27:26 rms-change max change #iterations 4.803495 187.6770 at 10iterations 2.412357 76.30892 at 20iterations 1.226566 36.41751 at 30iterations 0.6187284 18.43379 at 40iterations 0.3118194 9.015853 at 50iterations 0.1579886 5.077170 at 60iterations 7.9692915E-02 2.157414 at 70iterations 4.0387519E-02 1.211071 at 80iterations 2.0406092E-02 0.5858536 at 90iterations 1.0325059E-02 0.3178406 at 100iterations 5.2408767E-03 0.1518612 at 110iterations 2.6741393E-03 7.8277588E-02 at 120iterations finished qdiffx linear iterations at : 05:27:35 total time elapsed so far: 9.540000 # loops : 120 mean,max change (kT/e) : 2.6741393E-03 7.8277588E-02 energy calculations done at 9.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.730000 DelPhi exited at 05:27:35 9.735u 0.326s 0:10.52 95.5% 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 05:27:35 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 = 1986 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: 3.286221 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): -3.891000 44.85800 ymin,ymax (A): -22.31200 24.40800 zmin,zma (A): 5.566000 48.21200 x,y,z range (A): 48.74900 46.72000 42.64600 scale (grids/A): 3.286221 object centre (A): 20.48350 1.048000 26.88900 number of atom coordinates read : 1986 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.2470 centred at (gu) : 94.59180 86.56665 88.52728 assigned negative charge : -303.7472 centred at (gu) : 94.04849 87.15496 88.21236 start vw surface at 0.1400000 fill in re-entrant regions at 0.9900000 boundary points on vw surface= 181457 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17639 grid for indexing accessible points = 1.400000 m= 102718 mr = 134125 m= 44528 mr = 85713 m= 13391 mr = 36837 m= 2893 mr = 10592 m= 412 mr = 2108 m= 21 mr = 276 m= 0 mr = 4 time to grow re-entrant surface = 1.250000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.370000 number of dielectric boundary points 75765 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.520000 number of grid points assigned charge 15432 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) : 2.190814 object centre at (A) : 20.48350 1.048000 26.88900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1490837 0.1693026 midg,1,midg; midg,igrid,midg 0.4462431 -0.5170661 1,midg,midg; igrid,midg,midg 0.2751911 0.7628093 gauss-seidel spectral radius is 0.9993245 estimated iterations to convergence 303 setup time was (sec) 2.700000 now iterating at: 05:27:38 rms-change max change #iterations 10.57503 286.9930 at 10iterations 6.356116 161.9160 at 20iterations 3.813908 76.70766 at 30iterations 2.285960 45.69258 at 40iterations 1.365436 25.81671 at 50iterations 0.8122780 15.70947 at 60iterations 0.4829419 8.529945 at 70iterations 0.2867241 5.287360 at 80iterations 0.1701663 3.036628 at 90iterations 0.1009255 1.993320 at 100iterations 5.9781924E-02 1.032436 at 110iterations 3.5536859E-02 0.6146011 at 120iterations 2.1142351E-02 0.3851042 at 130iterations 1.2616252E-02 0.2288733 at 140iterations 7.6068430E-03 0.1599975 at 150iterations 4.6824035E-03 8.0390930E-02 at 160iterations 2.9595194E-03 5.3046227E-02 at 170iterations 1.9580286E-03 3.5655975E-02 at 180iterations finished qdiffx linear iterations at : 05:27:52 total time elapsed so far: 16.81000 # loops : 180 mean,max change (kT/e) : 1.9580286E-03 3.5655975E-02 energy calculations done at 16.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.99000 DelPhi exited at 05:27:53 16.996u 0.334s 0:17.72 97.7% 0+0k 0+0io 0pf+0w