Wed Nov 16 20:47:45 PST 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 Wed Nov 16 2011 at 20:47:45 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 ! Automatically converted by prot2crg.py # of charge parameter records: 952 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3109 !!! WARNING: TPO 162 has a net charge of -1.7500 !!! WARNING: TPO 301 has a net charge of -1.7500 !!! WARNING: SEP 320 has a net charge of -1.5000 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: 0.6026034 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): 7.679000 63.00700 ymin,ymax (A): 22.76800 81.84500 zmin,zma (A): 5.895000 61.21600 x,y,z range (A): 55.32800 59.07700 55.32100 scale (grids/A): 0.6026034 object centre (A): 35.34300 52.30650 33.55550 number of atom coordinates read : 3109 total number of charged atoms : 2959 net assigned charge : -16.00001 assigned positive charge : 455.1051 centred at (gu) : 89.26186 89.36907 89.07644 assigned negative charge : -471.1059 centred at (gu) : 89.38224 89.36119 88.83179 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7920 nv = 96 ne = 84 npr = 60600 no. pairs analyzed = 60600 no. exposed pairs = 4333 no. arc points = 31377 no. surface atoms = 1448 nbur = 1661 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 397 mr = 3986 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 4313 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3072 ## 270 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 9586 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3942937E-08 3.2117471E-09 midg,1,midg; midg,igrid,midg -8.8782066E-09 -6.0809664E-09 1,midg,midg; igrid,midg,midg -1.8961859E-09 -1.1196547E-08 gauss-seidel spectral radius is 0.9858102 estimated iterations to convergence 69 setup time was (sec) 0.4500000 now iterating at: 20:47:46 rms-change max change #iterations 0.1232751 19.01367 at 10iterations 1.1026740E-02 1.449767 at 20iterations 1.5422043E-03 0.2961807 at 30iterations 4.9001223E-04 9.6651077E-02 at 40iterations 1.9023057E-04 3.7956238E-02 at 50iterations finished qdiffx linear iterations at : 20:47:49 total time elapsed so far: 3.770000 # loops : 50 mean,max change (kT/e) : 1.9023057E-04 3.7956238E-02 energy calculations done at 3.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.910000 DelPhi exited at 20:47:49 3.918u 0.205s 0:04.41 93.1% 0+0k 0+46080io 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 Wed Nov 16 2011 at 20:47:49 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 ! Automatically converted by prot2crg.py # of charge parameter records: 952 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3109 !!! WARNING: TPO 162 has a net charge of -1.7500 !!! WARNING: TPO 301 has a net charge of -1.7500 !!! WARNING: SEP 320 has a net charge of -1.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.807810 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): 7.679000 63.00700 ymin,ymax (A): 22.76800 81.84500 zmin,zma (A): 5.895000 61.21600 x,y,z range (A): 55.32800 59.07700 55.32100 scale (grids/A): 1.807810 object centre (A): 35.34300 52.30650 33.55550 number of atom coordinates read : 3109 total number of charged atoms : 2959 net assigned charge : -16.00001 assigned positive charge : 455.1051 centred at (gu) : 87.78507 88.10635 87.22867 assigned negative charge : -471.1059 centred at (gu) : 88.14614 88.08325 86.49494 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 85356 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31377 grid for indexing accessible points = 1.400000 m= 29132 mr = 56216 m= 3830 mr = 20337 m= 170 mr = 1986 m= 3 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 105 time to turn everything in is 0.5100000 number of dielectric boundary points 39908 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 228 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 23186 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) : 0.6026034 object centre at (A) : 35.34300 52.30650 33.55550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.5799296E-02 2.2359209E-03 midg,1,midg; midg,igrid,midg -1.4817705E-02 -1.8815950E-02 1,midg,midg; igrid,midg,midg -1.7014824E-02 -4.3078039E-02 gauss-seidel spectral radius is 0.9985651 estimated iterations to convergence 209 setup time was (sec) 0.7300000 now iterating at: 20:47:50 rms-change max change #iterations 4.278015 189.1212 at 10iterations 1.960958 75.59943 at 20iterations 0.8920570 28.67448 at 30iterations 0.4102813 15.00105 at 40iterations 0.1876899 6.414912 at 50iterations 8.6048983E-02 2.948202 at 60iterations 3.9582431E-02 1.239719 at 70iterations 1.8374568E-02 0.6723035 at 80iterations 8.5836938E-03 0.2500973 at 90iterations 4.1437731E-03 0.1345882 at 100iterations 2.1064368E-03 7.9109192E-02 at 110iterations 1.1813686E-03 5.2612305E-02 at 120iterations finished qdiffx linear iterations at : 20:47:58 total time elapsed so far: 8.000000 # loops : 120 mean,max change (kT/e) : 1.1813686E-03 5.2612305E-02 energy calculations done at 8.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.140000 DelPhi exited at 20:47:58 8.144u 0.226s 0:08.66 96.5% 0+0k 0+45328io 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 Wed Nov 16 2011 at 20:47:58 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 ! Automatically converted by prot2crg.py # of charge parameter records: 952 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3109 !!! WARNING: TPO 162 has a net charge of -1.7500 !!! WARNING: TPO 301 has a net charge of -1.7500 !!! WARNING: SEP 320 has a net charge of -1.5000 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: 2.711715 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): 7.679000 63.00700 ymin,ymax (A): 22.76800 81.84500 zmin,zma (A): 5.895000 61.21600 x,y,z range (A): 55.32800 59.07700 55.32100 scale (grids/A): 2.711715 object centre (A): 35.34300 52.30650 33.55550 number of atom coordinates read : 3109 total number of charged atoms : 2959 net assigned charge : -16.00001 assigned positive charge : 455.1051 centred at (gu) : 86.67735 87.15923 85.84266 assigned negative charge : -471.1059 centred at (gu) : 87.21903 87.12462 84.74221 start vw surface at 0.1200000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 197425 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31377 grid for indexing accessible points = 1.400000 m= 95723 mr = 137470 m= 31853 mr = 75615 m= 6413 mr = 24400 m= 692 mr = 4268 m= 29 mr = 355 m= 0 mr = 3 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 410 time to turn everything in is 1.360000 number of dielectric boundary points 90024 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 23666 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) : 1.807810 object centre at (A) : 35.34300 52.30650 33.55550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6634138 7.9843283E-02 midg,1,midg; midg,igrid,midg -5.5912431E-02 -0.2189582 1,midg,midg; igrid,midg,midg -0.2640764 -0.3833478 gauss-seidel spectral radius is 0.9992639 estimated iterations to convergence 291 setup time was (sec) 1.590000 now iterating at: 20:48:00 rms-change max change #iterations 10.49535 317.5269 at 10iterations 6.233172 138.0570 at 20iterations 3.654022 77.30109 at 30iterations 2.132722 40.51242 at 40iterations 1.239447 25.92693 at 50iterations 0.7188694 13.95486 at 60iterations 0.4154370 7.222709 at 70iterations 0.2398477 4.349015 at 80iterations 0.1387180 3.066085 at 90iterations 8.0180608E-02 1.489838 at 100iterations 4.6222962E-02 0.7694397 at 110iterations 2.6737282E-02 0.4600334 at 120iterations 1.5443806E-02 0.2721722 at 130iterations 8.9791613E-03 0.1792383 at 140iterations 5.2575641E-03 0.1079998 at 150iterations 3.1418414E-03 7.3218346E-02 at 160iterations 1.9294019E-03 4.3382645E-02 at 170iterations 1.2469795E-03 2.7082443E-02 at 180iterations finished qdiffx linear iterations at : 20:48:11 total time elapsed so far: 13.25000 # loops : 180 mean,max change (kT/e) : 1.2469795E-03 2.7082443E-02 energy calculations done at 13.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.39000 DelPhi exited at 20:48:12 13.397u 0.226s 0:13.92 97.7% 0+0k 0+45320io 0pf+0w