Mon Oct 10 17:12:17 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 Mon Oct 10 2011 at 17:12:17 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2986 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: 0.6062670 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): 13.85300 70.72500 ymin,ymax (A): 3.829000 50.92400 zmin,zma (A): 6.930000 65.65000 x,y,z range (A): 56.87200 47.09500 58.72000 scale (grids/A): 0.6062670 object centre (A): 42.28900 27.37650 36.29000 number of atom coordinates read : 2986 total number of charged atoms : 2841 net assigned charge : -5.499976 assigned positive charge : 448.7409 centred at (gu) : 89.19084 90.39191 90.40017 assigned negative charge : -454.2421 centred at (gu) : 89.10757 90.49158 90.51482 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7298 nv = 96 ne = 84 npr = 59614 no. pairs analyzed = 59614 no. exposed pairs = 3906 no. arc points = 27785 no. surface atoms = 1328 nbur = 1658 mkacc time = 0.2000000 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 = 1.456000 m= 319 mr = 3774 m= 0 mr = 12 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.4000000 number of dielectric boundary points 3831 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2787 ## 293 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9132 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7863201E-09 -9.6254080E-09 midg,1,midg; midg,igrid,midg 2.1006366E-09 -8.7387590E-09 1,midg,midg; igrid,midg,midg -8.5621208E-09 1.2084279E-09 gauss-seidel spectral radius is 0.9859564 estimated iterations to convergence 69 setup time was (sec) 0.6700000 now iterating at: 17:12:18 rms-change max change #iterations 0.1192009 18.13905 at 10iterations 1.0500479E-02 1.443981 at 20iterations 8.9866930E-04 0.1322479 at 30iterations 7.9671961E-05 1.1581421E-02 at 40iterations 7.2302764E-06 1.0910034E-03 at 50iterations finished qdiffx linear iterations at : 17:12:22 total time elapsed so far: 4.800000 # loops : 50 mean,max change (kT/e) : 7.2302764E-06 1.0910034E-03 energy calculations done at 4.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.960000 DelPhi exited at 17:12:22 4.966u 0.383s 0:05.63 94.8% 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 17:12:22 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2986 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: 1.818801 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): 13.85300 70.72500 ymin,ymax (A): 3.829000 50.92400 zmin,zma (A): 6.930000 65.65000 x,y,z range (A): 56.87200 47.09500 58.72000 scale (grids/A): 1.818801 object centre (A): 42.28900 27.37650 36.29000 number of atom coordinates read : 2986 total number of charged atoms : 2841 net assigned charge : -5.499976 assigned positive charge : 448.7409 centred at (gu) : 87.57193 91.17492 91.19950 assigned negative charge : -454.2421 centred at (gu) : 87.32218 91.47432 91.54406 start vw surface at 0.1200000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 79613 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27785 grid for indexing accessible points = 1.400000 m= 25632 mr = 53405 m= 3244 mr = 17814 m= 139 mr = 1804 m= 3 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 984 time to turn everything in is 0.6400000 number of dielectric boundary points 35578 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 262 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 22238 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) : 0.6062670 object centre at (A) : 42.28900 27.37650 36.29000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0210043E-02 -4.5684399E-04 midg,1,midg; midg,igrid,midg -2.0354160E-03 -2.7025767E-02 1,midg,midg; igrid,midg,midg -4.1392740E-02 1.3763935E-02 gauss-seidel spectral radius is 0.9985538 estimated iterations to convergence 208 setup time was (sec) 0.9600000 now iterating at: 17:12:24 rms-change max change #iterations 4.210209 187.6133 at 10iterations 1.918669 67.03665 at 20iterations 0.8754756 32.14294 at 30iterations 0.3994943 13.16626 at 40iterations 0.1828977 5.861873 at 50iterations 8.3789743E-02 2.791687 at 60iterations 3.8218856E-02 1.257051 at 70iterations 1.7509645E-02 0.5681846 at 80iterations 8.0069108E-03 0.2623415 at 90iterations 3.6745919E-03 0.1142235 at 100iterations 1.6767149E-03 5.4428101E-02 at 110iterations 7.6614734E-04 2.1976471E-02 at 120iterations finished qdiffx linear iterations at : 17:12:35 total time elapsed so far: 12.07000 # loops : 120 mean,max change (kT/e) : 7.6614734E-04 2.1976471E-02 energy calculations done at 12.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.25000 DelPhi exited at 17:12:35 12.250u 0.430s 0:13.00 97.5% 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 Mon Oct 10 2011 at 17:12:35 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2986 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: 2.728202 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): 13.85300 70.72500 ymin,ymax (A): 3.829000 50.92400 zmin,zma (A): 6.930000 65.65000 x,y,z range (A): 56.87200 47.09500 58.72000 scale (grids/A): 2.728202 object centre (A): 42.28900 27.37650 36.29000 number of atom coordinates read : 2986 total number of charged atoms : 2841 net assigned charge : -5.499976 assigned positive charge : 448.7409 centred at (gu) : 86.35757 91.76235 91.79910 assigned negative charge : -454.2421 centred at (gu) : 85.98330 92.21134 92.31583 start vw surface at 0.1300000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 184530 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27785 grid for indexing accessible points = 1.400000 m= 86427 mr = 130568 m= 27512 mr = 68514 m= 5418 mr = 21003 m= 530 mr = 3764 m= 22 mr = 299 m= 0 mr = 4 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 3227 time to turn everything in is 1.670000 number of dielectric boundary points 80287 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 22722 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) : 1.818801 object centre at (A) : 42.28900 27.37650 36.29000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3233879 0.1889374 midg,1,midg; midg,igrid,midg -3.5304945E-02 -0.2743014 1,midg,midg; igrid,midg,midg -0.4655129 0.2744618 gauss-seidel spectral radius is 0.9992563 estimated iterations to convergence 289 setup time was (sec) 2.040000 now iterating at: 17:12:38 rms-change max change #iterations 10.31860 325.7101 at 10iterations 6.094433 142.4873 at 20iterations 3.554124 84.15611 at 30iterations 2.060499 42.57899 at 40iterations 1.195609 23.30184 at 50iterations 0.6897044 14.68837 at 60iterations 0.3981679 8.180956 at 70iterations 0.2288719 4.365924 at 80iterations 0.1316136 2.419177 at 90iterations 7.5708665E-02 1.755764 at 100iterations 4.3467663E-02 0.8351583 at 110iterations 2.5004219E-02 0.4529877 at 120iterations 1.4349074E-02 0.2969995 at 130iterations 8.2306284E-03 0.1561613 at 140iterations 4.7274358E-03 8.3921432E-02 at 150iterations 2.7088150E-03 5.2139282E-02 at 160iterations 1.5589348E-03 3.0522704E-02 at 170iterations 8.9674647E-04 1.9465446E-02 at 180iterations finished qdiffx linear iterations at : 17:13:00 total time elapsed so far: 23.66000 # loops : 180 mean,max change (kT/e) : 8.9674647E-04 1.9465446E-02 energy calculations done at 23.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.84000 DelPhi exited at 17:13:00 23.845u 0.546s 0:24.76 98.4% 0+0k 0+0io 0pf+0w