Mon Oct 10 22:41:52 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 22:41:52 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 = 2658 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: 0.5936005 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): 14.83100 74.80400 ymin,ymax (A): -9.476000 44.17300 zmin,zma (A): -8.288000 34.74700 x,y,z range (A): 59.97300 53.64900 43.03500 scale (grids/A): 0.5936005 object centre (A): 44.81750 17.34850 13.22950 number of atom coordinates read : 2658 total number of charged atoms : 2516 net assigned charge : 4.500016 assigned positive charge : 399.2907 centred at (gu) : 89.11311 89.39364 89.99523 assigned negative charge : -394.7914 centred at (gu) : 89.34691 89.51311 90.17636 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6030 nv = 96 ne = 84 npr = 54062 no. pairs analyzed = 54062 no. exposed pairs = 3178 no. arc points = 21777 no. surface atoms = 1074 nbur = 1584 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 289 mr = 3368 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 2925 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2136 ## 225 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7634 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.8770389E-09 -4.1338502E-09 midg,1,midg; midg,igrid,midg 5.8206577E-09 -1.8991255E-09 1,midg,midg; igrid,midg,midg 1.0314747E-08 -4.7197553E-09 gauss-seidel spectral radius is 0.9853163 estimated iterations to convergence 68 setup time was (sec) 0.5800000 now iterating at: 22:41:53 rms-change max change #iterations 0.1054819 17.95814 at 10iterations 9.3633588E-03 1.256115 at 20iterations 1.2105758E-03 0.2694435 at 30iterations 2.9049817E-04 7.5752258E-02 at 40iterations 8.1819846E-05 2.1415710E-02 at 50iterations finished qdiffx linear iterations at : 22:41:57 total time elapsed so far: 4.160000 # loops : 50 mean,max change (kT/e) : 8.1819846E-05 2.1415710E-02 energy calculations done at 4.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.340000 DelPhi exited at 22:41:57 4.341u 0.292s 0:05.70 81.2% 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 22:41:58 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 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2658 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: 1.780801 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): 14.83100 74.80400 ymin,ymax (A): -9.476000 44.17300 zmin,zma (A): -8.288000 34.74700 x,y,z range (A): 59.97300 53.64900 43.03500 scale (grids/A): 1.780801 object centre (A): 44.81750 17.34850 13.22950 number of atom coordinates read : 2658 total number of charged atoms : 2516 net assigned charge : 4.500016 assigned positive charge : 399.2907 centred at (gu) : 87.33875 88.18028 89.98482 assigned negative charge : -394.7914 centred at (gu) : 88.04026 88.53915 90.52908 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 67429 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21777 grid for indexing accessible points = 1.400000 m= 22081 mr = 47240 m= 2849 mr = 16195 m= 103 mr = 1713 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 570 time to turn everything in is 0.4900000 number of dielectric boundary points 27306 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 148 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 19590 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) : 0.5936005 object centre at (A) : 44.81750 17.34850 13.22950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2838568E-02 -6.6663815E-05 midg,1,midg; midg,igrid,midg 2.7108893E-02 -1.3674418E-02 1,midg,midg; igrid,midg,midg -3.1882559E-04 -5.0286636E-02 gauss-seidel spectral radius is 0.9984434 estimated iterations to convergence 201 setup time was (sec) 0.8200000 now iterating at: 22:41:59 rms-change max change #iterations 3.768644 162.1278 at 10iterations 1.671110 61.38206 at 20iterations 0.7441207 25.43387 at 30iterations 0.3302183 11.42981 at 40iterations 0.1474673 5.724495 at 50iterations 6.5523759E-02 2.128868 at 60iterations 2.9225087E-02 1.035289 at 70iterations 1.3167162E-02 0.4459915 at 80iterations 5.9578838E-03 0.2036896 at 90iterations 2.7431103E-03 9.2813492E-02 at 100iterations 1.3032764E-03 4.9892426E-02 at 110iterations 6.5068813E-04 2.9682159E-02 at 120iterations finished qdiffx linear iterations at : 22:42:07 total time elapsed so far: 9.370000 # loops : 120 mean,max change (kT/e) : 6.5068813E-04 2.9682159E-02 energy calculations done at 9.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.550000 DelPhi exited at 22:42:08 9.549u 0.275s 0:10.19 96.2% 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 22:42:08 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 = 2658 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: 2.671202 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): 14.83100 74.80400 ymin,ymax (A): -9.476000 44.17300 zmin,zma (A): -8.288000 34.74700 x,y,z range (A): 59.97300 53.64900 43.03500 scale (grids/A): 2.671202 object centre (A): 44.81750 17.34850 13.22950 number of atom coordinates read : 2658 total number of charged atoms : 2516 net assigned charge : 4.500016 assigned positive charge : 399.2907 centred at (gu) : 86.00806 87.27027 89.97721 assigned negative charge : -394.7914 centred at (gu) : 87.06036 87.80865 90.79355 start vw surface at 0.1400000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 156382 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21777 grid for indexing accessible points = 1.400000 m= 74761 mr = 114825 m= 23667 mr = 61116 m= 4898 mr = 18758 m= 446 mr = 3692 m= 9 mr = 261 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 1983 time to turn everything in is 1.250000 number of dielectric boundary points 61511 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 20122 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) : 1.780801 object centre at (A) : 44.81750 17.34850 13.22950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2526312 1.8777531E-02 midg,1,midg; midg,igrid,midg 0.2912498 -0.2153740 1,midg,midg; igrid,midg,midg -9.7603098E-02 -0.7982864 gauss-seidel spectral radius is 0.9992024 estimated iterations to convergence 280 setup time was (sec) 1.580000 now iterating at: 22:42:10 rms-change max change #iterations 9.121271 326.8687 at 10iterations 5.211775 130.9581 at 20iterations 2.956073 106.7782 at 30iterations 1.676377 42.38279 at 40iterations 0.9481459 18.29549 at 50iterations 0.5340419 10.08734 at 60iterations 0.3010823 6.194528 at 70iterations 0.1700946 3.494421 at 80iterations 9.5614061E-02 1.986122 at 90iterations 5.3872254E-02 1.039097 at 100iterations 3.0345345E-02 0.6357609 at 110iterations 1.7101301E-02 0.3363116 at 120iterations 9.6612573E-03 0.2015076 at 130iterations 5.4689222E-03 0.1174316 at 140iterations 3.1248010E-03 6.7935944E-02 at 150iterations 1.8046994E-03 3.7303925E-02 at 160iterations 1.0700211E-03 2.4604797E-02 at 170iterations 6.5150950E-04 1.6338348E-02 at 180iterations finished qdiffx linear iterations at : 22:42:23 total time elapsed so far: 15.00000 # loops : 180 mean,max change (kT/e) : 6.5150950E-04 1.6338348E-02 energy calculations done at 15.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.18000 DelPhi exited at 22:42:24 15.181u 0.290s 0:15.87 97.4% 0+0k 0+0io 0pf+0w