Sat Oct 8 16:31:19 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 8 2011 at 16:31:19 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 = 4403 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5437855 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): 15.53700 79.11200 ymin,ymax (A): 119.5320 184.9990 zmin,zma (A): -1.115000 59.89200 x,y,z range (A): 63.57500 65.46699 61.00700 scale (grids/A): 0.5437855 object centre (A): 47.32450 152.2655 29.38850 number of atom coordinates read : 4403 total number of charged atoms : 4233 net assigned charge : 5.500040 assigned positive charge : 674.2599 centred at (gu) : 92.03883 89.89757 87.63089 assigned negative charge : -668.7631 centred at (gu) : 92.02589 89.85429 87.66457 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8412 nv = 96 ne = 84 npr = 87775 no. pairs analyzed = 87775 no. exposed pairs = 5511 no. arc points = 38541 no. surface atoms = 1840 nbur = 2563 mkacc time = 0.1900000 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 = 1.568000 m= 371 mr = 4435 m= 0 mr = 21 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.4200000 number of dielectric boundary points 4327 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3934 ## 519 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 11178 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0942378E-09 4.9383127E-13 midg,1,midg; midg,igrid,midg -9.8668976E-11 6.7395728E-10 1,midg,midg; igrid,midg,midg 1.1382226E-10 6.9061179E-10 gauss-seidel spectral radius is 0.9826730 estimated iterations to convergence 63 setup time was (sec) 0.6400000 now iterating at: 16:31:20 rms-change max change #iterations 8.6844459E-02 13.64876 at 10iterations 6.2407488E-03 1.107658 at 20iterations 9.2510763E-04 0.1323814 at 30iterations 2.9445396E-04 3.8043976E-02 at 40iterations 1.0297551E-04 1.2933731E-02 at 50iterations finished qdiffx linear iterations at : 16:31:22 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 1.0297551E-04 1.2933731E-02 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 16:31:23 3.293u 0.189s 0:03.83 90.6% 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 8 2011 at 16:31:23 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 = 4403 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.631357 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): 15.53700 79.11200 ymin,ymax (A): 119.5320 184.9990 zmin,zma (A): -1.115000 59.89200 x,y,z range (A): 63.57500 65.46699 61.00700 scale (grids/A): 1.631357 object centre (A): 47.32450 152.2655 29.38850 number of atom coordinates read : 4403 total number of charged atoms : 4233 net assigned charge : 5.500040 assigned positive charge : 674.2599 centred at (gu) : 96.11549 89.69128 82.89145 assigned negative charge : -668.7631 centred at (gu) : 96.07706 89.56241 82.99355 start vw surface at 0.2000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 94053 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38541 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 30079 mr = 65112 m= 3462 mr = 20422 m= 97 mr = 1765 m= 0 mr = 5 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 644 time to turn everything in is 0.6600000 number of dielectric boundary points 40387 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 462 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 32383 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) : 0.5437855 object centre at (A) : 47.32450 152.2655 29.38850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.3884392E-03 7.9117324E-03 midg,1,midg; midg,igrid,midg 2.2875201E-02 3.1581342E-02 1,midg,midg; igrid,midg,midg -9.3915071E-03 -1.3047966E-02 gauss-seidel spectral radius is 0.9983261 estimated iterations to convergence 194 setup time was (sec) 0.9500000 now iterating at: 16:31:24 rms-change max change #iterations 4.178782 142.9665 at 10iterations 1.794146 64.78209 at 20iterations 0.7738200 25.98630 at 30iterations 0.3352774 10.48789 at 40iterations 0.1448107 5.048349 at 50iterations 6.2527359E-02 1.833107 at 60iterations 2.7122650E-02 0.8249435 at 70iterations 1.1796342E-02 0.3770714 at 80iterations 5.1693004E-03 0.1614990 at 90iterations 2.3363379E-03 7.0413589E-02 at 100iterations 1.0942897E-03 3.3072472E-02 at 110iterations 5.5144931E-04 1.7028809E-02 at 120iterations finished qdiffx linear iterations at : 16:31:31 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 5.5144931E-04 1.7028809E-02 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 16:31:31 7.750u 0.215s 0:08.26 96.3% 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 Sat Oct 8 2011 at 16:31:31 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 = 4403 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.447035 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): 15.53700 79.11200 ymin,ymax (A): 119.5320 184.9990 zmin,zma (A): -1.115000 59.89200 x,y,z range (A): 63.57500 65.46699 61.00700 scale (grids/A): 2.447035 object centre (A): 47.32450 152.2655 29.38850 number of atom coordinates read : 4403 total number of charged atoms : 4233 net assigned charge : 5.500040 assigned positive charge : 674.2599 centred at (gu) : 99.17306 89.53665 79.33692 assigned negative charge : -668.7631 centred at (gu) : 99.11553 89.34374 79.49019 start vw surface at 0.2000000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 218787 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38541 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 103086 mr = 159441 m= 30565 mr = 81124 m= 5458 mr = 22638 m= 410 mr = 3698 m= 3 mr = 188 m= 0 mr = 0 time to grow re-entrant surface = 0.9400001 no. cavity mid-points inaccessible to solvent = 2073 time to turn everything in is 1.600000 number of dielectric boundary points 91220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 44 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 33833 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) : 1.631357 object centre at (A) : 47.32450 152.2655 29.38850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8354041E-02 0.1622926 midg,1,midg; midg,igrid,midg 0.3726245 0.6063741 1,midg,midg; igrid,midg,midg -0.1315995 -0.2361616 gauss-seidel spectral radius is 0.9992135 estimated iterations to convergence 282 setup time was (sec) 1.910000 now iterating at: 16:31:33 rms-change max change #iterations 10.88443 408.6698 at 10iterations 6.339409 146.1167 at 20iterations 3.660629 80.06756 at 30iterations 2.104624 44.66109 at 40iterations 1.206070 23.28309 at 50iterations 0.6885098 12.92518 at 60iterations 0.3915667 7.356862 at 70iterations 0.2228426 4.049871 at 80iterations 0.1264098 2.229492 at 90iterations 7.1776427E-02 1.361782 at 100iterations 4.0634047E-02 0.7314835 at 110iterations 2.3057761E-02 0.3991804 at 120iterations 1.3078048E-02 0.2365036 at 130iterations 7.4068136E-03 0.1296439 at 140iterations 4.2296844E-03 7.5481415E-02 at 150iterations 2.4051375E-03 4.2881489E-02 at 160iterations 1.3887046E-03 2.9083252E-02 at 170iterations 8.1324804E-04 1.5796661E-02 at 180iterations finished qdiffx linear iterations at : 16:31:44 total time elapsed so far: 12.74000 # loops : 180 mean,max change (kT/e) : 8.1324804E-04 1.5796661E-02 energy calculations done at 12.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.91000 DelPhi exited at 16:31:45 12.917u 0.237s 0:13.45 97.6% 0+0k 0+0io 0pf+0w