Sat Oct 15 14:38:53 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 Sat Oct 15 2011 at 14:38:53 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 = 2753 !!! WARNING: PRO 352 has a net charge of 0.5000 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: 0.5630862 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): -13.87700 49.34600 ymin,ymax (A): -26.46200 17.55600 zmin,zma (A): -41.92800 5.544000 x,y,z range (A): 63.22300 44.01800 47.47200 scale (grids/A): 0.5630862 object centre (A): 17.73450 -4.453000 -18.19200 number of atom coordinates read : 2753 total number of charged atoms : 2614 net assigned charge : -0.9999737 assigned positive charge : 413.3694 centred at (gu) : 89.81578 89.65492 89.18167 assigned negative charge : -414.3704 centred at (gu) : 89.84647 89.51112 89.02787 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5755 nv = 96 ne = 84 npr = 54687 no. pairs analyzed = 54687 no. exposed pairs = 3589 no. arc points = 25655 no. surface atoms = 1205 nbur = 1548 mkacc time = 8.9999996E-02 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 = 1.540000 m= 223 mr = 2923 m= 0 mr = 5 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3050 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2647 ## 354 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 7416 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3215412E-09 1.3454049E-09 midg,1,midg; midg,igrid,midg -1.9361868E-09 1.4078526E-09 1,midg,midg; igrid,midg,midg 2.6964492E-10 -4.2946485E-10 gauss-seidel spectral radius is 0.9837152 estimated iterations to convergence 64 setup time was (sec) 0.4600000 now iterating at: 14:38:55 rms-change max change #iterations 8.1581809E-02 13.60522 at 10iterations 5.8520949E-03 1.098139 at 20iterations 4.1612345E-04 7.5715542E-02 at 30iterations 3.0821277E-05 4.9247742E-03 at 40iterations 2.2294885E-06 3.8099289E-04 at 50iterations finished qdiffx linear iterations at : 14:38:59 total time elapsed so far: 3.940000 # loops : 50 mean,max change (kT/e) : 2.2294885E-06 3.8099289E-04 energy calculations done at 3.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 14:39:00 4.082u 0.236s 0:06.43 67.0% 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 Sat Oct 15 2011 at 14:39:00 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 = 2753 !!! WARNING: PRO 352 has a net charge of 0.5000 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: 1.689259 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): -13.87700 49.34600 ymin,ymax (A): -26.46200 17.55600 zmin,zma (A): -41.92800 5.544000 x,y,z range (A): 63.22300 44.01800 47.47200 scale (grids/A): 1.689259 object centre (A): 17.73450 -4.453000 -18.19200 number of atom coordinates read : 2753 total number of charged atoms : 2614 net assigned charge : -0.9999737 assigned positive charge : 413.3694 centred at (gu) : 89.44659 88.96400 87.54418 assigned negative charge : -414.3704 centred at (gu) : 89.53906 88.53313 87.08344 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 63289 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25655 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18768 mr = 42066 m= 1867 mr = 12654 m= 46 mr = 915 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 1053 time to turn everything in is 0.3300000 number of dielectric boundary points 28328 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 286 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 20135 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) : 0.5630862 object centre at (A) : 17.73450 -4.453000 -18.19200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5509152E-02 5.5484227E-03 midg,1,midg; midg,igrid,midg -4.8830397E-03 3.2592751E-03 1,midg,midg; igrid,midg,midg 3.6096219E-03 4.2100921E-03 gauss-seidel spectral radius is 0.9982849 estimated iterations to convergence 192 setup time was (sec) 0.5800000 now iterating at: 14:39:01 rms-change max change #iterations 3.435511 163.3199 at 10iterations 1.461182 57.67549 at 20iterations 0.6245499 21.25543 at 30iterations 0.2655636 10.08561 at 40iterations 0.1136354 4.002663 at 50iterations 4.8470818E-02 1.831528 at 60iterations 2.0646790E-02 0.7203827 at 70iterations 8.8252155E-03 0.3198814 at 80iterations 3.7679761E-03 0.1376338 at 90iterations 1.6124685E-03 5.7768345E-02 at 100iterations 6.8772637E-04 2.6423395E-02 at 110iterations 2.9460114E-04 1.0654449E-02 at 120iterations finished qdiffx linear iterations at : 14:39:14 total time elapsed so far: 8.290000 # loops : 120 mean,max change (kT/e) : 2.9460114E-04 1.0654449E-02 energy calculations done at 8.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.430000 DelPhi exited at 14:39:15 8.433u 0.229s 0:15.01 57.6% 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 Sat Oct 15 2011 at 14:39:15 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 = 2753 !!! WARNING: PRO 352 has a net charge of 0.5000 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: 2.533888 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): -13.87700 49.34600 ymin,ymax (A): -26.46200 17.55600 zmin,zma (A): -41.92800 5.544000 x,y,z range (A): 63.22300 44.01800 47.47200 scale (grids/A): 2.533888 object centre (A): 17.73450 -4.453000 -18.19200 number of atom coordinates read : 2753 total number of charged atoms : 2614 net assigned charge : -0.9999737 assigned positive charge : 413.3694 centred at (gu) : 89.16982 88.44589 86.31610 assigned negative charge : -414.3704 centred at (gu) : 89.30846 87.79965 85.62509 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 147069 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25655 grid for indexing accessible points = 1.400000 m= 65760 mr = 103290 m= 18248 mr = 51340 m= 2754 mr = 13584 m= 180 mr = 1784 m= 6 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 3582 time to turn everything in is 0.7900000 number of dielectric boundary points 63933 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 20896 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) : 1.689259 object centre at (A) : 17.73450 -4.453000 -18.19200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1892171 9.0264164E-02 midg,1,midg; midg,igrid,midg -5.2111782E-02 3.0438127E-02 1,midg,midg; igrid,midg,midg 8.0862932E-02 0.4251134 gauss-seidel spectral radius is 0.9991680 estimated iterations to convergence 274 setup time was (sec) 1.060000 now iterating at: 14:39:21 rms-change max change #iterations 8.800392 391.8187 at 10iterations 4.960222 129.4355 at 20iterations 2.790471 69.34849 at 30iterations 1.564006 36.21144 at 40iterations 0.8723269 20.40806 at 50iterations 0.4883337 9.785767 at 60iterations 0.2716796 5.425484 at 70iterations 0.1511636 3.062212 at 80iterations 8.3979011E-02 2.001533 at 90iterations 4.6519924E-02 1.052010 at 100iterations 2.5843300E-02 0.5669899 at 110iterations 1.4346360E-02 0.2943554 at 120iterations 7.9686362E-03 0.1587524 at 130iterations 4.4200821E-03 8.8703394E-02 at 140iterations 2.4452733E-03 5.0389290E-02 at 150iterations 1.3616569E-03 2.6646376E-02 at 160iterations 7.5462903E-04 1.5043259E-02 at 170iterations 4.1842999E-04 9.7584724E-03 at 180iterations finished qdiffx linear iterations at : 14:39:45 total time elapsed so far: 12.91000 # loops : 180 mean,max change (kT/e) : 4.1842999E-04 9.7584724E-03 energy calculations done at 12.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.04000 DelPhi exited at 14:39:46 13.046u 0.246s 0:30.77 43.1% 0+0k 0+0io 0pf+0w