Mon Oct 10 09:14:09 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 09:14:09 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 = 1964 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: 0.6376044 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): -5.839000 35.33100 ymin,ymax (A): -3.713000 49.00500 zmin,zma (A): -24.53700 31.29700 x,y,z range (A): 41.17000 52.71800 55.83400 scale (grids/A): 0.6376044 object centre (A): 14.74600 22.64600 3.380001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 90.82932 92.53792 90.20457 assigned negative charge : -284.8263 centred at (gu) : 90.96385 92.65701 90.13985 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5612 nv = 96 ne = 84 npr = 39388 no. pairs analyzed = 39388 no. exposed pairs = 2524 no. arc points = 17977 no. surface atoms = 859 nbur = 1105 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 341 mr = 3123 m= 1 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2770 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1757 ## 172 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6454 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.1814399E-10 9.9507096E-09 midg,1,midg; midg,igrid,midg 8.0313018E-09 -9.3149577E-09 1,midg,midg; igrid,midg,midg 1.2514840E-08 -7.7681408E-09 gauss-seidel spectral radius is 0.9872054 estimated iterations to convergence 72 setup time was (sec) 0.3500000 now iterating at: 09:14:10 rms-change max change #iterations 0.1245287 20.07135 at 10iterations 1.2024931E-02 2.209187 at 20iterations 1.1934669E-03 0.2046618 at 30iterations 1.1522001E-04 2.0053864E-02 at 40iterations 1.1064421E-05 1.8520355E-03 at 50iterations finished qdiffx linear iterations at : 09:14:12 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 1.1064421E-05 1.8520355E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 09:14:13 3.397u 0.168s 0:03.85 92.2% 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 09:14:13 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.912813 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): -5.839000 35.33100 ymin,ymax (A): -3.713000 49.00500 zmin,zma (A): -24.53700 31.29700 x,y,z range (A): 41.17000 52.71800 55.83400 scale (grids/A): 1.912813 object centre (A): 14.74600 22.64600 3.380001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 92.48796 97.61372 90.61366 assigned negative charge : -284.8263 centred at (gu) : 92.89185 97.97116 90.41964 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 59820 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17977 grid for indexing accessible points = 1.400000 m= 23269 mr = 40940 m= 4138 mr = 17932 m= 255 mr = 3008 m= 1 mr = 114 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 1607 time to turn everything in is 0.3100000 number of dielectric boundary points 25489 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 114 iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 14418 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) : 0.6376044 object centre at (A) : 14.74600 22.64600 3.380001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4829618E-02 1.3894611E-02 midg,1,midg; midg,igrid,midg 2.8800493E-02 -6.9450117E-03 1,midg,midg; igrid,midg,midg 6.5542767E-03 -5.1903855E-03 gauss-seidel spectral radius is 0.9985741 estimated iterations to convergence 210 setup time was (sec) 0.5100000 now iterating at: 09:14:14 rms-change max change #iterations 3.584484 158.9011 at 10iterations 1.650017 57.49480 at 20iterations 0.7600833 28.72496 at 30iterations 0.3510346 13.09920 at 40iterations 0.1609193 6.210660 at 50iterations 7.4178867E-02 2.428234 at 60iterations 3.4113940E-02 1.189610 at 70iterations 1.5661770E-02 0.5293207 at 80iterations 7.2245938E-03 0.2363856 at 90iterations 3.3362426E-03 0.1217966 at 100iterations 1.5367927E-03 5.4503202E-02 at 110iterations 7.0459233E-04 2.3893118E-02 at 120iterations finished qdiffx linear iterations at : 09:14:21 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 7.0459233E-04 2.3893118E-02 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 09:14:21 7.752u 0.214s 0:08.35 95.3% 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 09:14:21 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.869220 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): -5.839000 35.33100 ymin,ymax (A): -3.713000 49.00500 zmin,zma (A): -24.53700 31.29700 x,y,z range (A): 41.17000 52.71800 55.83400 scale (grids/A): 2.869220 object centre (A): 14.74600 22.64600 3.380001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 93.73188 101.4206 90.92054 assigned negative charge : -284.8263 centred at (gu) : 94.33780 101.9568 90.62957 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 137934 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17977 grid for indexing accessible points = 1.400000 m= 72773 mr = 98783 m= 29233 mr = 60646 m= 7780 mr = 24680 m= 1149 mr = 6413 m= 72 mr = 872 m= 3 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 5520 time to turn everything in is 0.8000000 number of dielectric boundary points 57511 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 14656 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) : 1.912813 object centre at (A) : 14.74600 22.64600 3.380001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.091837 9.6582025E-03 midg,1,midg; midg,igrid,midg 0.2744402 -0.1026467 1,midg,midg; igrid,midg,midg 3.0713832E-02 -2.8982537E-02 gauss-seidel spectral radius is 0.9992313 estimated iterations to convergence 285 setup time was (sec) 1.030000 now iterating at: 09:14:22 rms-change max change #iterations 8.461235 442.9936 at 10iterations 4.865886 137.4483 at 20iterations 2.767340 63.26884 at 30iterations 1.575899 34.81859 at 40iterations 0.8973930 22.35027 at 50iterations 0.5091100 10.65708 at 60iterations 0.2891926 6.106504 at 70iterations 0.1646680 3.596565 at 80iterations 9.3057901E-02 1.952023 at 90iterations 5.2893575E-02 1.004896 at 100iterations 3.0005073E-02 0.6076202 at 110iterations 1.7036507E-02 0.3848834 at 120iterations 9.6356524E-03 0.1925077 at 130iterations 5.4654698E-03 0.1138725 at 140iterations 3.0951968E-03 6.4770699E-02 at 150iterations 1.7656694E-03 3.6281586E-02 at 160iterations 9.9931366E-04 1.9590855E-02 at 170iterations 5.6796568E-04 1.3381004E-02 at 180iterations finished qdiffx linear iterations at : 09:14:34 total time elapsed so far: 12.24000 # loops : 180 mean,max change (kT/e) : 5.6796568E-04 1.3381004E-02 energy calculations done at 12.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.38000 DelPhi exited at 09:14:34 12.383u 0.204s 0:12.85 97.8% 0+0k 0+0io 0pf+0w