Mon Oct 10 14:02:07 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 Mon Oct 10 2011 at 14:02:07 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3270 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: 0.5282604 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): -3.675000 63.71600 ymin,ymax (A): 15.81300 72.06300 zmin,zma (A): -13.49100 32.15800 x,y,z range (A): 67.39101 56.25000 45.64900 scale (grids/A): 0.5282604 object centre (A): 30.02050 43.93800 9.333501 number of atom coordinates read : 3270 total number of charged atoms : 3126 net assigned charge : -4.999991 assigned positive charge : 491.3967 centred at (gu) : 89.97884 87.39512 89.89490 assigned negative charge : -496.3979 centred at (gu) : 89.95194 87.39050 89.95670 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5880 nv = 96 ne = 84 npr = 66581 no. pairs analyzed = 66581 no. exposed pairs = 3991 no. arc points = 27461 no. surface atoms = 1357 nbur = 1913 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 232 mr = 3178 m= 0 mr = 3 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 2931 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2772 ## 386 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 7782 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.9155640E-11 -3.7140530E-10 midg,1,midg; midg,igrid,midg -3.2384143E-10 -7.0904782E-11 1,midg,midg; igrid,midg,midg -2.5192479E-10 -5.0833771E-11 gauss-seidel spectral radius is 0.9815561 estimated iterations to convergence 61 setup time was (sec) 0.6600000 now iterating at: 14:02:08 rms-change max change #iterations 6.7789875E-02 12.21118 at 10iterations 4.1382145E-03 0.7575641 at 20iterations 2.7640499E-04 4.2589188E-02 at 30iterations 3.1417479E-05 7.7590942E-03 at 40iterations 7.7780360E-06 2.1753311E-03 at 50iterations finished qdiffx linear iterations at : 14:02:12 total time elapsed so far: 4.500000 # loops : 50 mean,max change (kT/e) : 7.7780360E-06 2.1753311E-03 energy calculations done at 4.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.670000 DelPhi exited at 14:02:13 4.679u 0.384s 0:05.52 91.4% 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 Mon Oct 10 2011 at 14:02:13 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3270 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.584781 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): -3.675000 63.71600 ymin,ymax (A): 15.81300 72.06300 zmin,zma (A): -13.49100 32.15800 x,y,z range (A): 67.39101 56.25000 45.64900 scale (grids/A): 1.584781 object centre (A): 30.02050 43.93800 9.333501 number of atom coordinates read : 3270 total number of charged atoms : 3126 net assigned charge : -4.999991 assigned positive charge : 491.3967 centred at (gu) : 89.93586 82.18461 89.68407 assigned negative charge : -496.3979 centred at (gu) : 89.85522 82.17073 89.86958 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 66355 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27461 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 20071 mr = 46379 m= 1892 mr = 13777 m= 32 mr = 909 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 422 time to turn everything in is 0.5400000 number of dielectric boundary points 27285 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 365 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 23779 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) : 0.5282604 object centre at (A) : 30.02050 43.93800 9.333501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.6165068E-04 -4.1667833E-03 midg,1,midg; midg,igrid,midg -1.3662955E-02 -9.4721178E-03 1,midg,midg; igrid,midg,midg 6.0932781E-04 -4.5629353E-03 gauss-seidel spectral radius is 0.9980893 estimated iterations to convergence 182 setup time was (sec) 0.8700000 now iterating at: 14:02:14 rms-change max change #iterations 3.292076 164.9921 at 10iterations 1.338135 51.21610 at 20iterations 0.5459386 21.02529 at 30iterations 0.2240776 8.865975 at 40iterations 9.1602229E-02 3.272398 at 50iterations 3.7492439E-02 1.379805 at 60iterations 1.5258728E-02 0.5263748 at 70iterations 6.2498664E-03 0.2386138 at 80iterations 2.5562798E-03 9.3886137E-02 at 90iterations 1.0548810E-03 3.9359905E-02 at 100iterations 4.3561772E-04 1.6412735E-02 at 110iterations 1.8418016E-04 6.5183640E-03 at 120iterations finished qdiffx linear iterations at : 14:02:24 total time elapsed so far: 10.46000 # loops : 120 mean,max change (kT/e) : 1.8418016E-04 6.5183640E-03 energy calculations done at 10.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.64000 DelPhi exited at 14:02:24 10.646u 0.459s 0:11.52 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 Mon Oct 10 2011 at 14:02:24 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3270 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.377172 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): -3.675000 63.71600 ymin,ymax (A): 15.81300 72.06300 zmin,zma (A): -13.49100 32.15800 x,y,z range (A): 67.39101 56.25000 45.64900 scale (grids/A): 2.377172 object centre (A): 30.02050 43.93800 9.333501 number of atom coordinates read : 3270 total number of charged atoms : 3126 net assigned charge : -4.999991 assigned positive charge : 491.3967 centred at (gu) : 89.90350 78.27660 89.52599 assigned negative charge : -496.3979 centred at (gu) : 89.78271 78.25607 89.80429 start vw surface at 0.1300000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 154355 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27461 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 71012 mr = 113184 m= 18727 mr = 56486 m= 2898 mr = 13919 m= 170 mr = 1913 m= 3 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.8099999 no. cavity mid-points inaccessible to solvent = 1365 time to turn everything in is 1.330000 number of dielectric boundary points 61603 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 31 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 24971 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) : 1.584781 object centre at (A) : 30.02050 43.93800 9.333501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4263218E-02 -6.5699324E-02 midg,1,midg; midg,igrid,midg -0.2738654 -0.2114631 1,midg,midg; igrid,midg,midg 0.2996346 -0.1037134 gauss-seidel spectral radius is 0.9991078 estimated iterations to convergence 265 setup time was (sec) 1.650000 now iterating at: 14:02:27 rms-change max change #iterations 8.648615 284.5924 at 10iterations 4.792234 129.6564 at 20iterations 2.642679 62.14950 at 30iterations 1.458179 34.09918 at 40iterations 0.7993286 15.93812 at 50iterations 0.4386277 9.274437 at 60iterations 0.2391281 5.029132 at 70iterations 0.1305076 2.815042 at 80iterations 7.1205176E-02 1.414927 at 90iterations 3.8742706E-02 0.8363376 at 100iterations 2.1109035E-02 0.4748402 at 110iterations 1.1504970E-02 0.2316279 at 120iterations 6.2677902E-03 0.1322575 at 130iterations 3.4087426E-03 6.8104148E-02 at 140iterations 1.8583424E-03 3.7970066E-02 at 150iterations 1.0131104E-03 2.0694733E-02 at 160iterations 5.5363926E-04 1.0620594E-02 at 170iterations 3.0324757E-04 6.5207481E-03 at 180iterations finished qdiffx linear iterations at : 14:02:42 total time elapsed so far: 17.17000 # loops : 180 mean,max change (kT/e) : 3.0324757E-04 6.5207481E-03 energy calculations done at 17.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.34000 DelPhi exited at 14:02:43 17.349u 0.455s 0:18.17 97.9% 0+0k 0+0io 0pf+0w