Mon Oct 10 19:41:34 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 19:41:34 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 = 2507 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: 0.5913032 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): 1.689000 56.98100 ymin,ymax (A): -15.11900 34.34800 zmin,zma (A): 30.38700 90.59299 x,y,z range (A): 55.29200 49.46700 60.20599 scale (grids/A): 0.5913032 object centre (A): 29.33500 9.614502 60.49000 number of atom coordinates read : 2507 total number of charged atoms : 2370 net assigned charge : 7.500035 assigned positive charge : 366.4360 centred at (gu) : 89.33419 88.69274 91.25153 assigned negative charge : -358.9370 centred at (gu) : 89.38572 88.65305 91.25428 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5910 nv = 96 ne = 84 npr = 49575 no. pairs analyzed = 49575 no. exposed pairs = 3549 no. arc points = 25486 no. surface atoms = 1192 nbur = 1315 mkacc time = 9.0000004E-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 = 1.484000 m= 307 mr = 2840 m= 4 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3362 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2480 ## 276 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7311 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8783906E-09 3.0931013E-09 midg,1,midg; midg,igrid,midg 1.8389900E-09 2.5494113E-09 1,midg,midg; igrid,midg,midg 4.3254764E-09 9.4234320E-10 gauss-seidel spectral radius is 0.9852055 estimated iterations to convergence 67 setup time was (sec) 0.3800000 now iterating at: 19:41:35 rms-change max change #iterations 9.6310399E-02 14.02329 at 10iterations 7.8377482E-03 1.225594 at 20iterations 7.7416818E-04 0.1426868 at 30iterations 1.3799444E-04 2.9926300E-02 at 40iterations 3.7571208E-05 8.6860657E-03 at 50iterations finished qdiffx linear iterations at : 19:41:38 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 3.7571208E-05 8.6860657E-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) 3.380000 DelPhi exited at 19:41:38 3.388u 0.171s 0:04.07 87.2% 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 19:41:38 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 = 2507 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: 1.773910 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): 1.689000 56.98100 ymin,ymax (A): -15.11900 34.34800 zmin,zma (A): 30.38700 90.59299 x,y,z range (A): 55.29200 49.46700 60.20599 scale (grids/A): 1.773910 object centre (A): 29.33500 9.614502 60.49000 number of atom coordinates read : 2507 total number of charged atoms : 2370 net assigned charge : 7.500035 assigned positive charge : 366.4360 centred at (gu) : 88.00224 86.07767 93.75410 assigned negative charge : -358.9370 centred at (gu) : 88.15726 85.95930 93.76295 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 64170 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25486 grid for indexing accessible points = 1.400000 m= 20614 mr = 40914 m= 2810 mr = 14024 m= 132 mr = 1521 m= 0 mr = 27 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 31240 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 201 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 18416 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) : 0.5913032 object centre at (A) : 29.33500 9.614502 60.49000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1850912E-02 9.1903424E-04 midg,1,midg; midg,igrid,midg 1.3765970E-02 6.9157961E-03 1,midg,midg; igrid,midg,midg 2.1699691E-02 2.6992436E-02 gauss-seidel spectral radius is 0.9984332 estimated iterations to convergence 200 setup time was (sec) 0.5900000 now iterating at: 19:41:39 rms-change max change #iterations 3.529785 179.8406 at 10iterations 1.551115 64.99017 at 20iterations 0.6832341 22.74622 at 30iterations 0.3036658 11.23133 at 40iterations 0.1336612 4.505038 at 50iterations 5.9289537E-02 2.133202 at 60iterations 2.6301581E-02 0.9732037 at 70iterations 1.1698864E-02 0.4140024 at 80iterations 5.1711486E-03 0.1899261 at 90iterations 2.3366411E-03 8.2143784E-02 at 100iterations 1.0532733E-03 3.5064697E-02 at 110iterations 4.9109070E-04 1.8065453E-02 at 120iterations finished qdiffx linear iterations at : 19:41:47 total time elapsed so far: 8.790000 # loops : 120 mean,max change (kT/e) : 4.9109070E-04 1.8065453E-02 energy calculations done at 8.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.920000 DelPhi exited at 19:41:48 8.919u 0.251s 0:09.47 96.7% 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 19:41:48 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 = 2507 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: 2.660865 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): 1.689000 56.98100 ymin,ymax (A): -15.11900 34.34800 zmin,zma (A): 30.38700 90.59299 x,y,z range (A): 55.29200 49.46700 60.20599 scale (grids/A): 2.660865 object centre (A): 29.33500 9.614502 60.49000 number of atom coordinates read : 2507 total number of charged atoms : 2370 net assigned charge : 7.500035 assigned positive charge : 366.4360 centred at (gu) : 87.00320 84.11640 95.63116 assigned negative charge : -358.9370 centred at (gu) : 87.23602 83.93890 95.64438 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 148721 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25486 grid for indexing accessible points = 1.400000 m= 67965 mr = 100825 m= 22401 mr = 52671 m= 4644 mr = 16902 m= 543 mr = 3206 m= 27 mr = 308 m= 0 mr = 6 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8600000 number of dielectric boundary points 70383 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 18953 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) : 1.773910 object centre at (A) : 29.33500 9.614502 60.49000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4142793 -7.0879653E-02 midg,1,midg; midg,igrid,midg 0.2207399 7.9352044E-02 1,midg,midg; igrid,midg,midg 0.2055271 0.4952208 gauss-seidel spectral radius is 0.9992052 estimated iterations to convergence 280 setup time was (sec) 1.160000 now iterating at: 19:41:49 rms-change max change #iterations 8.713354 273.4034 at 10iterations 5.069582 144.8161 at 20iterations 2.908738 69.84968 at 30iterations 1.665208 35.67319 at 40iterations 0.9476020 21.35315 at 50iterations 0.5382386 11.58724 at 60iterations 0.3052943 7.228796 at 70iterations 0.1723233 3.482723 at 80iterations 9.7572312E-02 2.164452 at 90iterations 5.5100586E-02 1.280762 at 100iterations 3.1071898E-02 0.6548176 at 110iterations 1.7604500E-02 0.3781686 at 120iterations 9.9525722E-03 0.2212896 at 130iterations 5.6324941E-03 0.1141415 at 140iterations 3.1995345E-03 6.4454556E-02 at 150iterations 1.8302090E-03 3.6108971E-02 at 160iterations 1.0665039E-03 2.3814708E-02 at 170iterations 6.3375960E-04 1.6323090E-02 at 180iterations finished qdiffx linear iterations at : 19:42:01 total time elapsed so far: 12.88000 # loops : 180 mean,max change (kT/e) : 6.3375960E-04 1.6323090E-02 energy calculations done at 12.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.00000 DelPhi exited at 19:42:01 13.006u 0.283s 0:13.63 97.4% 0+0k 0+0io 0pf+0w