Tue Oct 11 05:25:23 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 Tue Oct 11 2011 at 05:25:23 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2189 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: 0.7431995 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): 25.70500 72.28900 ymin,ymax (A): -18.91500 28.98600 zmin,zma (A): 3.944000 46.44700 x,y,z range (A): 46.58400 47.90100 42.50300 scale (grids/A): 0.7431995 object centre (A): 48.99700 5.035501 25.19550 number of atom coordinates read : 2189 total number of charged atoms : 1910 net assigned charge : 7.500009 assigned positive charge : 307.8700 centred at (gu) : 88.98887 90.65774 90.21672 assigned negative charge : -300.3702 centred at (gu) : 89.13781 90.54183 90.29372 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7858 nv = 96 ne = 84 npr = 38728 no. pairs analyzed = 38728 no. exposed pairs = 2499 no. arc points = 17075 no. surface atoms = 856 nbur = 1333 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 616 mr = 4617 m= 2 mr = 142 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3717 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1478 ## 122 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8131 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0858963E-07 6.2618092E-08 midg,1,midg; midg,igrid,midg 1.8762709E-08 2.8905799E-07 1,midg,midg; igrid,midg,midg 3.4853747E-07 -1.0378375E-08 gauss-seidel spectral radius is 0.9905518 estimated iterations to convergence 84 setup time was (sec) 0.5200000 now iterating at: 05:25:23 rms-change max change #iterations 0.2424425 32.21464 at 10iterations 3.2894276E-02 4.108861 at 20iterations 4.7840620E-03 0.6060371 at 30iterations 8.1180676E-04 9.7614288E-02 at 40iterations 2.0308564E-04 2.1701813E-02 at 50iterations finished qdiffx linear iterations at : 05:25:26 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 2.0308564E-04 2.1701813E-02 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 05:25:27 3.558u 0.206s 0:04.17 89.9% 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 Tue Oct 11 2011 at 05:25:27 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2189 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: 2.229599 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): 25.70500 72.28900 ymin,ymax (A): -18.91500 28.98600 zmin,zma (A): 3.944000 46.44700 x,y,z range (A): 46.58400 47.90100 42.50300 scale (grids/A): 2.229599 object centre (A): 48.99700 5.035501 25.19550 number of atom coordinates read : 2189 total number of charged atoms : 1910 net assigned charge : 7.500009 assigned positive charge : 307.8700 centred at (gu) : 86.96658 91.97314 90.65032 assigned negative charge : -300.3702 centred at (gu) : 87.41364 91.62547 90.88109 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 81706 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17075 grid for indexing accessible points = 1.400000 m= 35963 mr = 58399 m= 8380 mr = 28014 m= 994 mr = 6050 m= 54 mr = 589 m= 0 mr = 20 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 34025 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 43 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 15214 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) : 0.7431995 object centre at (A) : 48.99700 5.035501 25.19550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8777357E-02 3.1130901E-02 midg,1,midg; midg,igrid,midg 5.4407097E-02 0.1089157 1,midg,midg; igrid,midg,midg 5.9578173E-02 -5.1238295E-02 gauss-seidel spectral radius is 0.9989235 estimated iterations to convergence 241 setup time was (sec) 1.000000 now iterating at: 05:25:28 rms-change max change #iterations 4.866650 167.9716 at 10iterations 2.482615 74.44903 at 20iterations 1.272242 35.95567 at 30iterations 0.6466168 18.90298 at 40iterations 0.3308181 9.285419 at 50iterations 0.1693373 5.091042 at 60iterations 8.6155266E-02 2.482330 at 70iterations 4.4266146E-02 1.214848 at 80iterations 2.2800844E-02 0.6352134 at 90iterations 1.1766980E-02 0.3121166 at 100iterations 6.1188280E-03 0.1805191 at 110iterations 3.2425427E-03 8.9683533E-02 at 120iterations finished qdiffx linear iterations at : 05:25:35 total time elapsed so far: 8.120000 # loops : 120 mean,max change (kT/e) : 3.2425427E-03 8.9683533E-02 energy calculations done at 8.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.310000 DelPhi exited at 05:25:36 8.311u 0.219s 0:08.97 94.9% 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 Tue Oct 11 2011 at 05:25:36 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2189 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: 3.344398 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): 25.70500 72.28900 ymin,ymax (A): -18.91500 28.98600 zmin,zma (A): 3.944000 46.44700 x,y,z range (A): 46.58400 47.90100 42.50300 scale (grids/A): 3.344398 object centre (A): 48.99700 5.035501 25.19550 number of atom coordinates read : 2189 total number of charged atoms : 1910 net assigned charge : 7.500009 assigned positive charge : 307.8700 centred at (gu) : 85.44994 92.95975 90.97539 assigned negative charge : -300.3702 centred at (gu) : 86.12045 92.43827 91.32171 start vw surface at 0.1300000 fill in re-entrant regions at 0.9000000 boundary points on vw surface= 187823 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17075 grid for indexing accessible points = 1.400000 m= 108057 mr = 139842 m= 49249 mr = 91237 m= 16400 mr = 41520 m= 4081 mr = 13345 m= 697 mr = 3194 m= 61 mr = 505 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 1.080000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.120000 number of dielectric boundary points 76686 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.260000 number of grid points assigned charge 15280 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) : 2.229599 object centre at (A) : 48.99700 5.035501 25.19550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1450877 0.2390158 midg,1,midg; midg,igrid,midg 0.4024100 0.7907433 1,midg,midg; igrid,midg,midg 0.5000551 -0.5657110 gauss-seidel spectral radius is 0.9993212 estimated iterations to convergence 303 setup time was (sec) 2.460000 now iterating at: 05:25:39 rms-change max change #iterations 10.61673 326.3541 at 10iterations 6.359001 119.5348 at 20iterations 3.796190 71.41650 at 30iterations 2.262563 43.22921 at 40iterations 1.348888 22.73979 at 50iterations 0.7980569 12.85017 at 60iterations 0.4736640 7.903507 at 70iterations 0.2808228 4.741366 at 80iterations 0.1662589 2.877806 at 90iterations 9.8305203E-02 1.590933 at 100iterations 5.8314726E-02 0.9918761 at 110iterations 3.4682225E-02 0.5645657 at 120iterations 2.0744281E-02 0.3597260 at 130iterations 1.2608232E-02 0.2291870 at 140iterations 7.8220246E-03 0.1298218 at 150iterations 5.0310190E-03 8.8365555E-02 at 160iterations 3.4256761E-03 5.7891846E-02 at 170iterations 2.4853917E-03 4.1297913E-02 at 180iterations finished qdiffx linear iterations at : 05:25:50 total time elapsed so far: 13.92000 # loops : 180 mean,max change (kT/e) : 2.4853917E-03 4.1297913E-02 energy calculations done at 13.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.11000 DelPhi exited at 05:25:51 14.115u 0.244s 0:14.65 97.9% 0+0k 0+0io 0pf+0w